From owner-chemistry@ccl.net Wed Oct 26 04:08:00 2005 From: "Noel O Boyle no228\a/cam.ac.uk" To: CCL Subject: CCL: W:Calculation of Point Group Message-Id: <-29743-051026040415-24868-KSvuA2Sy/W+X/LkBREO++g**server.ccl.net> X-Original-From: "Noel O'Boyle" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 26 Oct 2005 09:04:02 +0100 Mime-Version: 1.0 Sent to CCL by: "Noel O'Boyle" [no228]|[cam.ac.uk] Try looking at the source code, particularly the 'main' function (right at the end). It gives all the command-line options: Then try something like: ./symmetry -help Regards, Noel On Tue, 2005-10-25 at 13:16 -0500, Arindam Ganguly arindamganguly^gmail.com wrote: > Hi Huub, > i am not doing either of them. the Bloodshed Dev C++ IDE has compile > and run commmand in it. so i am compile the C source code and > executing it. it just gives me a black box. just like what we get in > windows command prompt, except the fact that in windows commad prompt > it mentions the path, but here nothing that sort of comes up. that's > why i was confused as to where is the mistake. i hope this helps, > thanks, > > Arindam > > On 10/25/05, Van Dam, HJJ (Huub) h.j.j.vandam|*|dl.ac.uk > wrote: > > Sent to CCL by: "Van Dam, HJJ \(Huub > \)" [h.j.j.vandam===dl.ac.uk] > Hi, > > Are you running this from the windows command prompt or are > you double > clicking it? > > Huub > > -----Original Message----- > > From: owner-chemistry#,#ccl.net > [mailto:owner-chemistry#,#ccl.net] > Sent: 24 October 2005 19:34 > To: Vandam, Huub > Subject: CCL: W:Calculation of Point Group > > Hi Serguei, > i went to the mentioned website and downloaded the symmetry.c > file. i am > using Bloodshed Dev C++ IDE, it can handle C files too. i > build the file > and execute but all it does is give a black command prompt > box, just > like we the one we get in WinXp. i don;t understand the > mistake i am > committing. > further i thought probably the zip files would be the updated > version > but same thing happened. could you plz tell what is mistake i > am making. > thanks= > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, > please change look up the X-Original-From: line in the mail > header. > > E-mail to subscribers: CHEMISTRY/./ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST/./ccl.net or use> > > Before posting check wait time for next message at: > http://www.ccl.net> > > > From owner-chemistry@ccl.net Wed Oct 26 04:43:00 2005 From: "Van Dam, HJJ \(Huub\) h.j.j.vandam#,#dl.ac.uk" To: CCL Subject: CCL: W:Calculation of Point Group Message-Id: <-29744-051026042103-30191-sE6WzyCvqjwHI3qz0yvukw#,#server.ccl.net> X-Original-From: "Van Dam, HJJ \(Huub\)" Content-Class: urn:content-classes:message Content-Transfer-Encoding: 7bit Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C5DA06.2DA5FB14" Date: Wed, 26 Oct 2005 09:20:51 +0100 MIME-Version: 1.0 Sent to CCL by: "Van Dam, HJJ \(Huub\)" [h.j.j.vandam{}dl.ac.uk] This is a multi-part message in MIME format. ------_=_NextPart_001_01C5DA06.2DA5FB14 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Arindam, =20 If I create a file called flop.txt to contain: =20 2 6 0.0 0.0 0.0 6 1.0 0.0 0.0 =20 with the program edit under windows and then run from the windows command prompt the command=20 =20 symmetry.exe flop.txt =20 The program nicely finds Dinfh as the point group. However I do get the behaviour you described if I run =20 symmetry.exe =20 or if I simply double click the executable. I.e. the program really needs to be invoked with the file containing the geometry on the command line (perhaps a nice enhancement would be for the program to print the usage information if it was invoked without any command line arguments). =20 Can you check that this works for you, please? =20 Huub =20 =20 ________________________________ > From: owner-chemistry{:}ccl.net [mailto:owner-chemistry{:}ccl.net]=20 Sent: 25 October 2005 19:16 To: Vandam, Huub Subject: CCL: W:Calculation of Point Group Hi Huub, i am not doing either of them. the Bloodshed Dev C++ IDE has compile and run commmand in it. so i am compile the C source code and executing it. it just gives me a black box. just like what we get in windows command prompt, except the fact that in windows commad prompt it mentions the path, but here nothing that sort of comes up. that's why i was confused as to where is the mistake. i hope this helps, thanks, Arindam On 10/25/05, Van Dam, HJJ (Huub) h.j.j.vandam|*|dl.ac.uk wrote:=20 Sent to CCL by: "Van Dam, HJJ \(Huub\)" [h.j.j.vandam=3D=3D=3Ddl.ac.uk] Hi, =09 Are you running this from the windows command prompt or are you double clicking it? =09 Huub =09 -----Original Message----- > From: owner-chemistry#,#ccl.net [mailto:owner-chemistry# ,#ccl.net] Sent: 24 October 2005 19:34 To: Vandam, Huub Subject: CCL: W:Calculation of Point Group =09 Hi Serguei, i went to the mentioned website and downloaded the symmetry.c file. i am using Bloodshed Dev C++ IDE, it can handle C files too. i build the file=20 and execute but all it does is give a black command prompt box, just like we the one we get in WinXp. i don;t understand the mistake i am committing. further i thought probably the zip files would be the updated version=20 but same thing happened. could you plz tell what is mistake i am making. thanks=3D =09 =09 =09 -=3D This is automatically added to each message by the mailing script =3D-=20 =09=09 E-mail to subscribers: CHEMISTRY/./ccl.net or use:=20=09 E-mail to administrators: CHEMISTRY-REQUEST/./ccl.net or use=09=20 =09 Before posting check wait time for next message at: http://www.ccl.net =09=09http://www.ccl.net/spammers.txt =09 =09=09 =09 =09 =09 ------_=_NextPart_001_01C5DA06.2DA5FB14 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
Hi Arindam,
 
If I create a file called flop.txt to=20 contain:
 
2
6 0.0 0.0 0.0
6 1.0 0.0 0.0
 
with the program edit under windows and then = run from the=20 windows command prompt the command
 
    symmetry.exe = flop.txt
 
The program nicely finds Dinfh as the point = group. However=20 I do get the behaviour you described if I run
 
    symmetry.exe
 
or if I simply double click the executable. = I.e. the=20 program really needs to be invoked with the file containing the geometry = on the=20 command line (perhaps a nice enhancement would be for the program to = print the=20 usage information if it was invoked without any command line=20 arguments).
 
Can you check that this works for you,=20 please?
 
Huub
 
 

From: owner-chemistry{:}ccl.net=20 [mailto:owner-chemistry{:}ccl.net]
Sent: 25 October 2005=20 19:16
To: Vandam, Huub
Subject: CCL: = W:Calculation=20 of Point Group

Hi Huub,
i am not doing either of them. the Bloodshed Dev = C++ IDE=20 has compile and run commmand in it. so i am compile the C source code = and=20 executing it. it just gives me a black box. just like what we get in = windows=20 command prompt, except the fact that in windows commad prompt it = mentions the=20 path, but here nothing that sort of comes up. that's why i was confused = as to=20 where is the mistake. i hope this helps, thanks,

Arindam

On 10/25/05, Van Dam, HJJ=20 (Huub) h.j.j.vandam|*|dl.ac.uk <owner-chemistry/./ccl.net&g= t;=20 wrote:=20

Sent=20 to CCL by: "Van Dam, HJJ \(Huub\)" = [h.j.j.vandam=3D=3D=3Ddl.ac.uk]
Hi,

Are=20 you running this from the windows command prompt or are you = double
clicking=20 it?

Huub

-----Original Message-----
> From:=20 owner-chemistry#,#ccl.net [mailto:owner-chemistry# = ,#ccl.net]
Sent: 24=20 October 2005 19:34
To: Vandam, Huub
Subject: CCL: W:Calculation = of Point=20 Group

Hi Serguei,
i went to the mentioned website and = downloaded the=20 symmetry.c file. i am
using Bloodshed Dev C++ IDE, it can handle C = files=20 too. i build the file
and execute but all it does is give a black = command=20 prompt box, just
like we the one we get in WinXp. i don;t = understand the=20 mistake i am
committing.
further i thought probably the zip = files would=20 be the updated version
but same thing happened. could you plz tell = what is=20 mistake i am making.
thanks=3D



-=3D This is = automatically added=20 to each message by the mailing script =3D-
To recover the email = address of=20 the author of the message, please change look up the = X-Original-From:=20 line in the mail header.

E-mail to subscribers: CHEMISTRY/./ccl.net or use:=20
      http://www.ccl.n= et/cgi-bin/ccl/send_ccl_message

E-mail=20 to administrators: CHEMISTRY-REQUEST/./ccl.net = or=20 use
      http://www.ccl.n= et/cgi-bin/ccl/send_ccl_message

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------_=_NextPart_001_01C5DA06.2DA5FB14-- From owner-chemistry@ccl.net Wed Oct 26 05:17:00 2005 From: "Konrad Hinsen khinsen:-:cea.fr" To: CCL Subject: CCL: W:Re: CCL: help needed Message-Id: <-29745-051026033514-22857-bzQCqE8FTruU3rS6kyKiyQ[-]server.ccl.net> X-Original-From: "Konrad Hinsen" Sent to CCL by: "Konrad Hinsen" [khinsen^^^cea.fr] On 25.10.2005, at 05:34, Dr Seth Olsen s.olsen1(_)uq.edu.au wrote: Also, anything written in python should be platform-independent, and in principle should be able to be set up under windows. Although I have never used MMTK under windows, you might give it a look to see if it can be used. If not under windows per se, than it almost certainly can be set up under cygwin. MMTK can run minimizations, but right now CHARMM MMTK works both natively under Windows (there's a binary installer that goes with the Windows distribution of Python) and with cygwin (install from the source code distribution). -- ------------------------------------------------------------------------------- Konrad Hinsen Laboratoire Leon Brillouin (CEA-CNRS), CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khinsen~!~cea.fr ------------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Oct 26 08:40:00 2005 From: "Brent Krueger kruegerb..hope.edu" To: CCL Subject: CCL: cubegen problem in G03 Message-Id: <-29746-051026031152-14154-MDMtl2eAvCAuyDFWKge/5A- -server.ccl.net> X-Original-From: Brent Krueger Content-Type: multipart/alternative; boundary=Apple-Mail-3--474038754 Date: Wed, 26 Oct 2005 01:28:20 -0400 Mime-Version: 1.0 (Apple Message framework v734) Sent to CCL by: Brent Krueger [kruegerb%x%hope.edu] --Apple-Mail-3--474038754 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi Yubo, Have you actually tried the cube keyword and gotten an error? I'm pretty sure that the cube keyword does actually still work even though the Gaussian manual tells you otherwise. You could try running it without the 'cards' keyword. This will generate a default cubefile and does not require you to enter any of the information defining the aspects of the cubefile. I'm positive that the cubegen procedure outlined by the Gaussian manual does NOT work for transition densities. I believe this is because the transition information is not stored in the formatted checkpoint file that is required by cubegen. If you have access to QChem, you might try that instead. Defining the spatial properties of the density require a bit more care in QChem than in Gaussian, but on the plus side QChem actually does what it says it should do; Gaussian does not. Good luck, Brent On Oct 25, 2005, at 5:41 PM, Yubo Fan yubofan~~mail.chem.tamu.edu wrote: > Hi, everyone, > > I've done some CIS calculations about some chromophores with G03. > Then I've got some problems to generate density transition cube > files with cubegen. I've got some references but the results were > calculated with G94. > > In G94 > > #p CIS(read,direct,Nstates=2)/3-21G* pop=reg scf=direct guess= > (read,only) density=(transition=1,check) geom=check nosymm cube= > (density,full,cards) > > can generate the cube files based on the previous CIS calculations. > > BUT, in G03, the keywork cube is not available, so I have to > utilize cubegen program (I guess it's better). In the command line, > I input "cubegen 0 Density=SCF test.fchk test.cube 0 h". Is the > INPUT correct compared to G94? If not, what should I type in? > > Thanks in advance, > > Yubo > ============================================================ > Dr. Yubo Fan Email: yubofan()mail.chem.tamu.edu > Department of Chemistry Tel: 1-979-845-5237 > Texas A&M University > College Station, TX 77843 > ============================================================ > __________________________________________________________________ Brent P. Krueger phone: 616 395 7629 Assistant Professor fax: 616 395 7118 Hope College Department of Chemistry Holland, MI 49423 --Apple-Mail-3--474038754 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Hi Yubo,

Have you actually tried the = cube keyword and gotten an error?=A0 I'm pretty sure that the cube = keyword does actually still work even though the Gaussian manual tells = you otherwise.=A0 You could try running it without the 'cards' keyword.=A0= This will generate a default cubefile and does not require you to enter = any of the information defining the aspects of the = cubefile.

I'm positive that the = cubegen procedure outlined by the Gaussian manual does NOT work for = transition densities.=A0 I believe this is because the transition = information is not stored in the formatted checkpoint file that is = required by cubegen.


If you have access to = QChem, you might try that instead.=A0 Defining the spatial properties of = the density require a bit more care in QChem than in Gaussian, but on = the plus side QChem actually does what it says it should do; Gaussian = does not.


Good = luck,
Brent



On Oct 25, = 2005, at 5:41 PM, Yubo Fan yubofan~~mail.chem.tamu.edu wrote:

Hi, everyone,
=A0
I've done some CIS calculations about some = chromophores with G03. Then I've got some problems to generate density = transition cube files with cubegen. I've got some references but the = results were calculated with G94.
=A0
In G94
=A0
=A0
=A0
=A0
=A0
Dr. Yubo Fan=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 Email: Department of Chemistry=A0=A0=A0 Tel:=A0=A0 = 1-979-845-5237
Texas A&M University


__________________________________________________________________=
Brent P. Krueger =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 phone: =A0 =A0 = 616 395 7629
Assistant = Professor=A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 fax:=A0 =A0 =A0 = =A0 =A0 =A0 616 395 7118
Hope = College
Department of = Chemistry
Holland, MI =A0 =A0 49423
=

= --Apple-Mail-3--474038754-- From owner-chemistry@ccl.net Wed Oct 26 09:14:00 2005 From: "Goedele Roos groos,vub.ac.be" To: CCL Subject: CCL: solvated H3O+ Message-Id: <-29747-051026083533-22821-9y8lZ6cOS35/0Ivd9sMR8A!=!server.ccl.net> X-Original-From: Goedele Roos Date: Wed, 26 Oct 2005 14:35:16 +0200 (CEST) Sent to CCL by: Goedele Roos [groos : vub.ac.be] Dear all, How can you calculate the energy of H3O+ in solution? I always get an error (conserning the cavity) using PCM. Thanks in advance for help. Goedele Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17 From owner-chemistry@ccl.net Wed Oct 26 09:49:00 2005 From: "Connie Chang cc236]~[ccmr.cornell.edu" To: CCL Subject: CCL: help finding sources Message-Id: <-29748-051026020239-9060-8CYoqGM3wqANpczOnkKPNA++server.ccl.net> X-Original-From: Connie Chang Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 26 Oct 2005 01:13:30 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Connie Chang [cc236*o*ccmr.cornell.edu] Hi all, Could anyone point me to good sources for Franck-Condon factors? Thanks in advance, Connie From owner-chemistry@ccl.net Wed Oct 26 10:24:00 2005 From: "David J Anick david.anick*rcn.com" To: CCL Subject: CCL: rigid scan in Gaussian Message-Id: <-29749-051025224202-29677-8AKrr6SREPAtA3AQ+InO6w a server.ccl.net> X-Original-From: "David J Anick" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0058_01C5D9B4.9A4E71A0" Date: Tue, 25 Oct 2005 22:36:55 -0400 MIME-Version: 1.0 Sent to CCL by: "David J Anick" [david.anick!^!rcn.com] This is a multi-part message in MIME format. ------=_NextPart_000_0058_01C5D9B4.9A4E71A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Mima, I have studied multiple proton transfers along water wires with ab initio methods. When I tried to do what you are suggesting, namely to use one O -- H distance as the independent variable for a PES and to relax the others -- it NEVER worked. In fact, I couldn't even get close to the transition state(s) this way. In my experience you'll have to fix at least two variables at a time and generate a 2-D PES. If you figure out something else, let me know. Some references: Anick, DJ, Ab Initio Study of an H24O12 Zwitterion, J. Phys. Chem. A, = 107 (2003), 1348-1357. Anick, DJ, Comparison of Octameric and Decameric Water Zwitterions, J. = Molec. Struct. (Theochem), 574 (2001), 109-115. Hope this is helpful, David Anick PhD MD ----- Original Message -----=20 From: Mima Staikova mima.staikova _ gmail.com=20 To: Anick, David =20 Sent: Tuesday, October 25, 2005 12:17 PM Subject: CCL: rigid scan in Gaussian Hi everyone, I need to model a reaction path of hydrogen abstraction, mediated by = water molecule. A hydrogen from the substrate is transferred to the water molecule = and simultaneously one of the water hydrogens is transferred to the = acceptor. I am interested in the energy along this pathway without = reoptimizing the substrate and the acceptor at every step along the = reaction coordinate. The reaction coordinate is a straight line.=20 The Scan keyword (rigid scan) is going to give me a potential surface, = not a potential curve, if I specify the coordinates of the two = hydrogens, that are moving simultaneously, calculating at every = coordinate change of the first H the all the changes for the second H.=20 How can I do the calculation in such a way that I have for each change = in the first H distance to the substrate just one change in the distance = for the second hydrogen, without having to resort to multiple single = point calculations?=20 Thank you. Mima Staikova ------=_NextPart_000_0058_01C5D9B4.9A4E71A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Mima,
 
I have studied multiple proton = transfers along=20 water wires
with ab initio = methods.
 
When I tried to do what you are = suggesting, namely=20 to
use one O -- H distance as the = independent variable=20 for
a PES and to relax the others -- it = NEVER=20 worked.
In fact, I couldn't even get close to = the=20 transition state(s)
this way.  In my experience you'll = have to fix=20 at least two
variables at a time and generate a 2-D = PES. =20 If you figure
out something else, let me = know.
 
Some references:
 
----- Original Message -----
From:=20 Mima=20 Staikova mima.staikova _ gmail.com
Sent: Tuesday, October 25, 2005 = 12:17=20 PM
Subject: CCL: rigid scan in=20 Gaussian

Hi everyone,

I need to model a reaction path of = hydrogen=20 abstraction, mediated by water molecule.
A hydrogen from  the=20 substrate is transferred to the  water molecule and = simultaneously one of=20 the water hydrogens is transferred to the acceptor. I am interested in = the=20 energy along this pathway without reoptimizing the substrate and the = acceptor=20 at every step along the reaction coordinate. The reaction coordinate = is a=20 straight line.

The Scan keyword (rigid scan) is going to give = me a=20 potential surface, not a potential curve, if I specify the coordinates = of the=20 two hydrogens, that are moving simultaneously, calculating at every = coordinate=20 change of the first H the all the changes for the second H. =

How can I=20 do the calculation in such a way that I have for each change in the = first H=20 distance to the substrate just one change in the distance for the = second=20 hydrogen, without having to resort to multiple single point = calculations?=20

Thank you.
Mima = Staikova



------=_NextPart_000_0058_01C5D9B4.9A4E71A0-- From owner-chemistry@ccl.net Wed Oct 26 10:59:00 2005 From: "Miguel Angel Pardo mapardo-*-iqfr.csic.es" To: CCL Subject: CCL: Problem with symmetry Message-Id: <-29750-051026070103-1258-UGt1podhaaXxBSBoNzkyUQ[-]server.ccl.net> X-Original-From: "Miguel Angel Pardo" Sent to CCL by: "Miguel Angel Pardo" [mapardo],[iqfr.csic.es] I am trying to optimize a big system that consists of four identical molecules using a DFT method. The system show a clearly C4h symmetry and I would like G03 could recognize this symmetry. However, the program find several mismatches between the atoms and the symmetry is turned off. The message that appeared: Mismatch for IA= 1 IOp= 2 Frag= 1 JA= 46 Frag= 4 Mismatch for IA= 2 IOp= 2 Frag= 1 JA= 47 Frag= 4 Mismatch for IA= 3 IOp= 2 Frag= 1 JA= 48 Frag= 4 Mismatch for IA= 4 IOp= 2 Frag= 1 JA= 49 Frag= 4 ... ... ... ... ... ... Mismatch for IA= 57 IOp= 2 Frag= 4 JA= 12 Frag= 1 Mismatch for IA= 58 IOp= 2 Frag= 4 JA= 13 Frag= 1 Mismatch for IA= 59 IOp= 2 Frag= 4 JA= 14 Frag= 1 Mismatch for IA= 60 IOp= 2 Frag= 4 JA= 15 Frag= 1 Symmetry turned off in CkCPSy: fragments do not conform to real system point group. I have tried Symmetry option with all the possibilities(Loose,Tight) but it did not work, and the geommetry is perfect symmetrical. From owner-chemistry@ccl.net Wed Oct 26 11:34:00 2005 From: "Nuno A. G. Bandeira nuno.bandeira%x%ist.utl.pt" To: CCL Subject: CCL: help needed Message-Id: <-29751-051025234000-24524-+ybpW+XdPKBbkNKIEMN4BA..server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Wed, 26 Oct 2005 04:03:19 +0100 Mime-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira[]ist.utl.pt] Perry E. Metzger perry^piermont.com wrote: > Microsoft also has a similar offering that they give away called > (inexplicably) "Services for Unix". I've heard they're getting rid of > it though. > > Performance under Cygwin will not rival performance on a real Linux > box -- Windows has architectural issues that make it perform pretty > badly in general, and Cygwin is just a POSIX scrim over Windows. This is a false issue. If the program were natively compiled in Windows the performance would be different. Problem is not many take the trouble to make their programs transferable to microsoft platforms. Many have never heard of Visual Studio .NET or even care to think of anything non-unix. Tha fault is on them not the OS itself. -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student # IST,Lisbon -- -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.361 / Virus Database: 267.12.5/147 - Release Date: 24-10-2005 From owner-chemistry@ccl.net Wed Oct 26 12:10:00 2005 From: "=?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= FB153746%ATIL.CEA.FR" To: CCL Subject: CCL: Frequencies with Gaussian03 + PBC Message-Id: <-29752-051026102357-25114-HxjZhPvHZpN2K99ziqu/lg _ server.ccl.net> X-Original-From: =?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C5DA38.DCC0A0C4" Date: Wed, 26 Oct 2005 16:23:40 +0200 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= [FB153746 ~ ATIL.CEA.FR] This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C5DA38.DCC0A0C4 Content-Type: text/plain; charset="iso-8859-1" Dear Gaussian03 Users, Is it possible to compute frequencies, and Raman + IR intensities with the PBC keyword ? Best regards, Frederic ------_=_NextPart_001_01C5DA38.DCC0A0C4 Content-Type: text/html; charset="iso-8859-1" Message
Dear Gaussian03 Users,
 
Is it possible to compute frequencies, and Raman + IR intensities with the PBC keyword ?
 
Best regards,
 
Frederic
 
------_=_NextPart_001_01C5DA38.DCC0A0C4-- From owner-chemistry@ccl.net Wed Oct 26 12:45:00 2005 From: "andras.borosy(!)givaudan.com" To: CCL Subject: CCL: reliable basis sets for PCM? Message-Id: <-29753-051026094306-3739-862VEDOYFbUERS9ntaaudQ::server.ccl.net> X-Original-From: andras.borosy_+_givaudan.com Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1" Date: Wed, 26 Oct 2005 15:42:58 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy::givaudan.com Dear Colleagues, What are the minimal basis sets in HF and DFT which give reliable Gibs` free energy values of drug-like organic molecules in simple solvents by using PCM? Many thank, Dr. András Borosy Seniour Scientist Delivery Systems, Fragrance Research Givaudan Schweiz AG Ueberlandstr. 138 8600 Dübendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy a givaudan.com From owner-chemistry@ccl.net Wed Oct 26 13:20:01 2005 From: "Sebastian Rohrer sebastian.rohrer . mail.uni-wuerzburg.de" To: CCL Subject: CCL: Run computational chemistry software (e.g. OpenEye Programs) parallel using PVM Message-Id: <-29754-051026113831-5837-h/982r25HND5dlc134li0w*server.ccl.net> X-Original-From: Sebastian Rohrer Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 26 Oct 2005 17:38:27 +0200 MIME-Version: 1.0 Sent to CCL by: Sebastian Rohrer [sebastian.rohrer/a\mail.uni-wuerzburg.de] Hi all, has anyone ever set up PVM in a heterogenous environment of Linux/Win computers in order to run computational chemistry programs? I am especially interested in doing this with FRED and OMEGA. The problem is, I'm rather no network geek and find the PVM- documentation on the web very difficult to understand. If anybody has ever done a thing like this, I would be very grateful for some help. Greetings, Sebastian -- Sebastian Rohrer AK Baumann - Molecular Modelling Group Department of Pharmaceutical Chemistry Institute of Pharmacy and Food Chemistry University of Wuerzburg Am Hubland 97074 Wuerzburg Germany From owner-chemistry@ccl.net Wed Oct 26 13:55:00 2005 From: "Wayne Steinmetz WES04747 ~ pomona.edu" To: CCL Subject: CCL: help finding sources Message-Id: <-29755-051026112115-644-6+E8RpCG4r9qfMCmEHcfpA[A]server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 26 Oct 2005 08:17:48 -0700 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747!A!pomona.edu] Paul H. Krupenie published comprehensive reviews of the molecular spectroscopy of O2,N2, and CO. These critical reviews contain tabulations of Franck-Condon factors for these molecules. O2, J. Phys. Chem. Ref. Data, Volume 1, pp. 423-534 (1972) N2, J. Phys. Chem. Ref. Data, Volume 6, pp. 113-307 (1977) CO, a NIST(NBS) publication, NSRDS-NBS 5 (1966) Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-707-7726 Email: wsteinmetz=-=pomona.edu WWW: pages.pomona.edu/~wsteinmetz -----Original Message----- > From: owner-chemistry=-=ccl.net [mailto:owner-chemistry=-=ccl.net] Sent: Tuesday, October 25, 2005 9:14 PM To: Wayne Steinmetz Subject: CCL: help finding sources Sent to CCL by: Connie Chang [cc236*o*ccmr.cornell.edu] Hi all, Could anyone point me to good sources for Franck-Condon factors? Thanks in advance, Conniehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software. From owner-chemistry@ccl.net Wed Oct 26 14:30:00 2005 From: "jmmckel]=[attglobal.net jmmckel]=[attglobal.net" To: CCL Subject: CCL: help finding sources Message-Id: <-29756-051026114737-18194-bdq0JDAV4heSV8GMhZU1Bw\a/server.ccl.net> X-Original-From: "jmmckel-#-attglobal.net" Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=iso-8859-1 Date: Wed, 26 Oct 2005 11:05:20 -0400 MIME-Version: 1.0 Sent to CCL by: "jmmckel---attglobal.net" [jmmckel---attglobal.net] Connie, Could I ask what you are working on? Cheers, John McKelvey Original Message: ----------------- > From: Connie Chang cc236]~[ccmr.cornell.edu owner-chemistry(!)ccl.net Date: Wed, 26 Oct 2005 01:13:30 -0400 (EDT) To: jmmckel(!)attglobal.net Subject: CCL: help finding sources Sent to CCL by: Connie Chang [cc236*o*ccmr.cornell.edu] Hi all, Could anyone point me to good sources for Franck-Condon factors? Thanks in advance, Conniehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From owner-chemistry@ccl.net Wed Oct 26 15:05:00 2005 From: "Yubo Fan yubofan#,#mail.chem.tamu.edu" To: CCL Subject: CCL: cubegen problem in G03 Message-Id: <-29757-051026105351-19241-oBfYFyiLMIutNRBlFp2Kjw/./server.ccl.net> X-Original-From: "Yubo Fan" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0012_01C5DA13.27E092B0" Date: Wed, 26 Oct 2005 09:53:45 -0500 MIME-Version: 1.0 Sent to CCL by: "Yubo Fan" [yubofan*o*mail.chem.tamu.edu] This is a multi-part message in MIME format. ------=_NextPart_000_0012_01C5DA13.27E092B0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dr. Krueger, I haven't tried the keyword, cube, with G03 yet because I didn't find it = in the manual. I tried it a few minutes ago and it worked. Thank you = very much. I also doubted the cubegen program didn't work correctly = since I didn't see reasonable density visualizations on either Chem3D or = GaussView. That's why I submitted a message to CCL. Now I have one more question about the unit in your programs. I think I = should use Bohr instead of Angstrom. I also checked the Cartesian in the = output files and it is also in Bohr. So, is there an option available in = your program to convert the unit into Angstrom? I appreciate for your patience. BTW, my wife and I stopped by Holland = and added some gas last Saturday. My wife rotated from Midland, MI to = Freeport, TX at Dow. I really wanted to visit you but I needed to come = back to work on Monday. Regards, Yubo ----- Original Message -----=20 From: Brent Krueger kruegerb..hope.edu=20 To: Fan, Yubo =20 Sent: Wednesday, October 26, 2005 12:28 AM Subject: CCL: cubegen problem in G03 Hi Yubo, Have you actually tried the cube keyword and gotten an error? I'm = pretty sure that the cube keyword does actually still work even though = the Gaussian manual tells you otherwise. You could try running it = without the 'cards' keyword. This will generate a default cubefile and = does not require you to enter any of the information defining the = aspects of the cubefile. I'm positive that the cubegen procedure outlined by the Gaussian = manual does NOT work for transition densities. I believe this is = because the transition information is not stored in the formatted = checkpoint file that is required by cubegen. If you have access to QChem, you might try that instead. Defining the = spatial properties of the density require a bit more care in QChem than = in Gaussian, but on the plus side QChem actually does what it says it = should do; Gaussian does not. Good luck, Brent On Oct 25, 2005, at 5:41 PM, Yubo Fan yubofan~~mail.chem.tamu.edu = wrote: Hi, everyone, I've done some CIS calculations about some chromophores with G03. = Then I've got some problems to generate density transition cube files = with cubegen. I've got some references but the results were calculated = with G94. In G94 #p CIS(read,direct,Nstates=3D2)/3-21G* pop=3Dreg scf=3Ddirect = guess=3D(read,only) density=3D(transition=3D1,check) geom=3Dcheck nosymm = cube=3D(density,full,cards) can generate the cube files based on the previous CIS calculations. BUT, in G03, the keywork cube is not available, so I have to utilize = cubegen program (I guess it's better). In the command line, I input = "cubegen 0 Density=3DSCF test.fchk test.cube 0 h". Is the INPUT correct = compared to G94? If not, what should I type in? Thanks in advance, Yubo = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dr. Yubo Fan Email: yubofan()mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-5237 Texas A&M University College Station, TX 77843 = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D __________________________________________________________________ Brent P. Krueger phone: 616 395 7629 Assistant Professor fax: 616 395 7118 Hope College Department of Chemistry Holland, MI 49423 ------=_NextPart_000_0012_01C5DA13.27E092B0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dr. = Krueger,
 
I haven't tried the keyword, = cube, with=20 G03 yet because I didn't find it in the manual. I tried it a few = minutes=20 ago and it worked. Thank you very much. I also doubted the cubegen = program=20 didn't work correctly since I didn't see reasonable density = visualizations on=20 either Chem3D or GaussView. That's why I submitted a message to=20 CCL.
 
Now I have one more question about = the unit in=20 your programs. I think I should use Bohr instead of Angstrom. I also = checked=20 the Cartesian in the output files and it is also in Bohr. So, = is there=20 an option available in your program to convert the unit into=20 Angstrom?
 
I appreciate for your patience. = BTW, my wife=20 and I stopped by Holland and added some gas last Saturday. My wife = rotated from=20 Midland, MI to Freeport, TX at Dow. I really wanted to visit you but I = needed to=20 come back to work on Monday.
 
Regards,
 
Yubo

Anick, DJ, Ab Initio Study of an=20 H24O12 Zwitterion, J. Phys. Chem. A, = 107=20 (2003), 1348-1357.

Anick, DJ, Comparison of Octameric = and=20 Decameric Water Zwitterions, J. Molec. Struct. (Theochem), = 574=20 (2001), 109-115.

 

Hope this is helpful,
David Anick PhD=20 MD
----- Original Message -----
From:=20 Brent=20 Krueger kruegerb..hope.edu
Sent: Wednesday, October 26, = 2005 12:28=20 AM
Subject: CCL: cubegen problem = in=20 G03

Hi Yubo,

Have you actually tried the cube keyword and gotten an = error?  I'm=20 pretty sure that the cube keyword does actually still work even though = the=20 Gaussian manual tells you otherwise.  You could try running it = without=20 the 'cards' keyword.  This will generate a default cubefile and = does not=20 require you to enter any of the information defining the aspects of = the=20 cubefile.

I'm positive that the cubegen procedure outlined by the Gaussian = manual=20 does NOT work for transition densities.  I believe this is = because the=20 transition information is not stored in the formatted checkpoint file = that is=20 required by cubegen.


If you have access to QChem, you might try that instead.  = Defining=20 the spatial properties of the density require a bit more care in QChem = than in=20 Gaussian, but on the plus side QChem actually does what it says it = should do;=20 Gaussian does not.


Good luck,
Brent



On Oct 25, 2005, at 5:41 PM, Yubo Fan yubofan~~mail.chem.tamu.edu = wrote:

Hi,=20 everyone,
 
I've done some CIS = calculations=20 about some chromophores with G03. Then I've got some problems to = generate=20 density transition cube files with cubegen. I've got some references = but the=20 results were calculated with G94.
 
In = G94
 
#p=20 CIS(read,direct,Nstates=3D2)/3-21G* pop=3Dreg scf=3Ddirect = guess=3D(read,only)=20 density=3D(transition=3D1,check) geom=3Dcheck nosymm=20 cube=3D(density,full,cards)
 
can=20 generate the cube files based on the previous CIS=20 calculations.
 
BUT, in=20 G03, the keywork cube is not available, so I have to utilize cubegen = program=20 (I guess it's better). In the command line, I input "cubegen 0 = Density=3DSCF=20 test.fchk test.cube 0 h". Is the INPUT correct compared to G94? If = not, what=20 should I type in?
 
Thanks in=20 advance,
 
Yubo
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3DDr. Yubo=20 = Fan           &nbs= p;  =20 Email: yubofan()mail.chem.tamu.eduDepartment of=20 Chemistry    Tel:   = 1-979-845-5237Texas A&M=20 University
College=20 Station, TX 77843=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

________________________________________________________________= __
Brent P. Krueger   =    =20                   = phone:=20     616 395=20 7629
Assistant Professor  =  =20                 = fax:          =  =20 616 395 7118
Hope College
Department of Chemistry
Holland, MI     = = 49423

= ------=_NextPart_000_0012_01C5DA13.27E092B0-- From owner-chemistry@ccl.net Wed Oct 26 15:40:00 2005 From: "chemical reactivity chemreac---vub.ac.be" To: CCL Subject: CCL: Chemical Reactivity Symposium, Brussels, April 5-7, 2006 Message-Id: <-29758-051026103619-8791-rXia8BH+rVdq9qlwJXAGtQ],[server.ccl.net> X-Original-From: "chemical reactivity" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 26 Oct 2005 15:56:27 +0200 MIME-Version: 1.0 Sent to CCL by: "chemical reactivity" [chemreac]-[vub.ac.be] Dear Colleague, A Three Day International Symposium will be held on (Theoretical Aspects of) of "Chemical Reactivity", at the Vrije Universiteit Brussel, Brussels, Belgium, from April 5 to 7, 2006. This Symposium is organized under the auspices of the Fund for Scientific Research Flanders and the International Solvay Institutes for Physics and Chemistry. The aim of the conference is to give the audience an impression of theoretical aspects of chemical reactivity, as it can now be studied starting from the electronic structure of atoms, molecules,... using a variety of quantum mechanical methodologies. Both more fundamental and applied aspects (wave function vs. DFT reactivity descriptors, dynamics, aromaticity, organic and inorganic reactions, biosystems, zeolites, ...) will be addressed. For this purpose 13 internationally renowned speakers will deliver invited talks (40 minutes each) on various approaches/applications. Contributed lectures will be given by a selected number of foreign participants and representatives of a number of Belgian research groups. A poster session will give ample space and time for presentation of research results by all other participants. The invited speakers (all confirmed) are : P. W. Ayers (McMaster University Hamilton, Ontario, Canada ) P. K. Chattaraj ( Indian Institute of Technology, Kharagpur, India) D. A. Dixon ( The University of Alabama ,Tuscaloosa, USA) W. Domcke (Lehrstuhl für Theoretische Chemie, Garching, Germany) P. W. Fowler ( University of Sheffield, Sheffield, UK) J. Hutter (Universität Zürich, Zürich, Switzerland) J.M.L. Martin (Weizmann Institute of Science, Rechovot, Israel) R. G. Parr ( University of North Carolina, Chapel Hill, USA) U. Röthlisberger (Ecole Polytechnique Federale, Lausanne,Switzerland) M. Solà ( Universitat de Girona, Girona, Spain) M. Sprik ( University of Cambridge, United Kingdom ) R.A. van Santen (Eindhoven Technical University,The Netherlands ) P. von Rague Schleyer ( University of Georgia, Athens, USA) Full details as well as the Registration and Abstract Submission form can be found on the website http://www.vub.ac.be/chemicalreactivity/ Looking forward to meet you in Brussels, with very best regards, Paul Geerlings Chair of the Organizing Committee Prof. P. GEERLINGS Free University of Brussels Faculty of Sciences Department of General Chemistry (ALGC) Pleinlaan 2 1050 Brussels Belgium Tel. : +32.2.629.33.14 Fax. : +32.2.629.33.17 e-mail : pgeerlin%vub.ac.be From owner-chemistry@ccl.net Wed Oct 26 16:15:00 2005 From: "Jim Kress ccl_nospam]![kressworks.com" To: CCL Subject: CCL:G: Filters Message-Id: <-29759-051026131557-7532-b5jV6HPwIGkbk8FWemJGzw .. server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 26 Oct 2005 13:14:28 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam%kressworks.com] Is there any way to set up a subscriber defined CCL filter to screen out all the requests for help on Gaussian products? In the face of Gaussian's refusal to provide adequate support of the products (developed with taxpayer money) they sell (at exorbitant prices), I am sick and tired of repeatedly having to manually delete each and every plea for help from frustrated Gaussian users. Any help would be appreciated. Regards, Jim Kress "The reformation was preceded by the discovery of America, as if the Almighty graciously meant to open a sanctuary to the persecuted in future years, when home should afford neither friendship nor safety." -- Thomas Paine (Common Sense, 1776) From owner-chemistry@ccl.net Wed Oct 26 17:25:01 2005 From: "Perry E. Metzger perry[#]piermont.com" To: CCL Subject: CCL: help needed Message-Id: <-29760-051026143842-28461-gxIXHjLJ+AkdkT3+BChMdQ : server.ccl.net> X-Original-From: "Perry E. Metzger" Content-Type: text/plain; charset=us-ascii Date: Wed, 26 Oct 2005 14:38:30 -0400 MIME-Version: 1.0 Sent to CCL by: "Perry E. Metzger" [perry]=[piermont.com] "Nuno A. G. Bandeira" writes: > Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira[]ist.utl.pt] > Perry E. Metzger perry^piermont.com wrote: > >> Microsoft also has a similar offering that they give away called >> (inexplicably) "Services for Unix". I've heard they're getting rid of >> it though. >> Performance under Cygwin will not rival performance on a real Linux >> box -- Windows has architectural issues that make it perform pretty >> badly in general, and Cygwin is just a POSIX scrim over Windows. > > This is a false issue. If the program were natively compiled in > Windows the performance would be different. Problem is not many take > the trouble to make their programs transferable to microsoft > platforms. Many have never heard of Visual Studio .NET or even care to > think of anything non-unix. Tha fault is on them not the OS itself. Sadly, you are wrong on this. Windows has a number of very serious design flaws, especially in things like the virtual memory management subsystem, which seriously compromise performance. For example, it is difficult to do the sort of "memory for disk I/O" tradeoff that you do on most Unix systems under Windows because the ability to tune buffer cache policy is extremely limited. It is easy to put Windows into situations where it becomes I/O bound even though there is enormous amounts of memory available for caching. If you insist on arguing about this with me, I suggest you do it off the list -- most of the people here aren't going to be interested in the intimate details. However, the fact here are straightforward. I've studied the issue very carefully. Windows just doesn't perform well in a wide variety of cases interesting to people who do computational chemistry. It is also expensive. There is no good reason to use it on machines that crunch numbers for a living, and there are excellent reasons *not* to use it. Perry From owner-chemistry@ccl.net Wed Oct 26 18:00:00 2005 From: "Ohyun Kwon ok16_-_mail.gatech.edu" To: CCL Subject: CCL:G: g98 geometry optimization under electric field Message-Id: <-29761-051026115804-24787-9npsmt30WZS6VIpp5HwFtA###server.ccl.net> X-Original-From: Ohyun Kwon Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 26 Oct 2005 10:58:02 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Ohyun Kwon [ok16]^[mail.gatech.edu] Dear CClers; I did geometry optimization under series of electric field strngths by G98 to compare with the experiment. But, it is shown that I have to apply much stronger electric field to get some agreement with experimental results which are Raman intensities. For example, the experiment is done at the electric field of 0.0001 au, but the meaningful calculation results are appeared at the lectric field of 0.1 au. I would grealty appreciate it if you would kindly explain about this matter. Thank you very much for your kind attention in advance. Yours, Tommy Tommy Ohyun Kwon, Ph.D School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta Georgia, 30332 Email: ohyun.kwon]-[chemistry.gatech.edu From owner-chemistry@ccl.net Wed Oct 26 18:35:00 2005 From: "Bahadr Altnta altintas_b*|*ibu.edu.tr" To: CCL Subject: CCL: About the simulate layer spaces Message-Id: <-29762-051026145356-5332-5tHrVfTFXE04V4vaWBcYyQ~~server.ccl.net> X-Original-From: "Bahadr Altnta" Sent to CCL by: "Bahadr Altnta" [altintas_b(_)ibu.edu.tr] is there any method to simulate the change in distance of layer spaces when a metal get into two graphite like layers. I'm new at this computational and need to get advice of it... thanx From owner-chemistry@ccl.net Wed Oct 26 19:45:01 2005 From: "Robinson, James James.Robinson(_)evotec.com" To: CCL Subject: CCL: reliable basis sets for PCM? Message-Id: <-29764-051026154924-22301-VIGG9D0YaIO6PlWNpvW6TA#%#server.ccl.net> X-Original-From: "Robinson, James" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 26 Oct 2005 20:03:57 +0100 MIME-Version: 1.0 Sent to CCL by: "Robinson, James" [James.Robinson\a/evotec.com] I have found 6-31+G(d) and aug-cc-pVDZ to be okay for PCM calcs with B3lyp and HF. Anions certainly diffuse and polarisation. To get delta G values suitable for thermodynamic pKa I have used b3lyp/6-311+G(2d,p) with CPCM. Dr J Robinson -----Original Message----- > From: owner-chemistry~~ccl.net [mailto:owner-chemistry~~ccl.net] Sent: 26 October 2005 14:43 To: Robinson, James Subject: CCL: reliable basis sets for PCM? Sent to CCL by: andras.borosy::givaudan.com Dear Colleagues, What are the minimal basis sets in HF and DFT which give reliable Gibs` free energy values of drug-like organic molecules in simple solvents by using PCM? Many thank, Dr. András Borosy Seniour Scientist Delivery Systems, Fragrance Research Givaudan Schweiz AG Ueberlandstr. 138 8600 Dübendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy ~ givaudan.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Oct 26 20:20:00 2005 From: "Robinson, James James.Robinson-$-evotec.com" To: CCL Subject: CCL: solvated H3O+ Message-Id: <-29765-051026154922-22258-U8S5dE6NcecHXrJ3Sk0TsA%a%server.ccl.net> X-Original-From: "Robinson, James" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 26 Oct 2005 20:05:31 +0100 MIME-Version: 1.0 Sent to CCL by: "Robinson, James" [James.Robinson^^evotec.com] Try CPCM, it includes two additional solvation terms compared to PCM. James -----Original Message----- > From: owner-chemistry/a\ccl.net [mailto:owner-chemistry/a\ccl.net] Sent: 26 October 2005 13:35 To: Robinson, James Subject: CCL: solvated H3O+ Sent to CCL by: Goedele Roos [groos : vub.ac.be] Dear all, How can you calculate the energy of H3O+ in solution? I always get an error (conserning the cavity) using PCM. Thanks in advance for help. Goedele Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Oct 26 20:55:01 2005 From: "N. Sukumar nagams===rpi.edu" To: CCL Subject: CCL:G: Filters Message-Id: <-29766-051026192015-14602-2MTQrrCjPpMNMDctfVFAzQ ~~ server.ccl.net> X-Original-From: "N. Sukumar" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Wed, 26 Oct 2005 19:20:02 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams%a%rpi.edu] It should be a trivial matter to do this in whichever mail utility you use. Many Gaussian questions posted here are from those who WILL not read a manual, but many are useful to others; and if by "taxpayer money" you refer to the program's origins at a public university, the same could be said of almost every popular computational chemistry program, most search engines and, if you include other sources of taxpayer funds, even electronic computers and the internet itself. Disclaimer: I have no connection with Gaussian except as a user. -- ****************************************************** Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute ****************************************************** Jim Kress ccl_nospam]![kressworks.com wrote: >Sent to CCL by: "Jim Kress" [ccl_nospam%kressworks.com] >Is there any way to set up a subscriber defined CCL filter to screen out all >the requests for help on Gaussian products? In the face of Gaussian's >refusal to provide adequate support of the products (developed with taxpayer >money) they sell (at exorbitant prices), I am sick and tired of repeatedly >having to manually delete each and every plea for help from frustrated >Gaussian users. > >Any help would be appreciated. > >Regards, > >Jim Kress > >"The reformation was preceded by the discovery of America, as if the >Almighty graciously meant to open a sanctuary to the persecuted in future >years, when home should afford neither friendship nor safety." -- Thomas >Paine (Common Sense, 1776)> > > > > > > From owner-chemistry@ccl.net Wed Oct 26 21:30:00 2005 From: "janl{}speakeasy.net" To: CCL Subject: CCL:G: filters Message-Id: <-29767-051026211154-23434-arV/gxoTxj61pvkooAFIlA;;server.ccl.net> X-Original-From: janl!^!speakeasy.net Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 27 Oct 2005 01:11:45 +0000 MIME-Version: 1.0 Sent to CCL by: janl||speakeasy.net Dear CCL, For those who want to quickly identify messages on Gaussian I added a G: string to messages that contain: "gaussian", "g98", "g03" (case insensitive) in the body. So now, once you see the subject line starting from: CCL:G: you will know that the message contains one (or more) of these words. You can even redirect it to another folder using procmail... Jan From owner-chemistry@ccl.net Wed Oct 26 22:05:00 2005 From: "Brian Salter-Duke b_duke(0)octa4.net.au" To: CCL Subject: CCL:G: Filters Message-Id: <-29768-051026203507-26505-SyWYTT1KPiFQ4gR8sXBuvQ_._server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 27 Oct 2005 08:06:32 +1000 Mime-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke:octa4.net.au] On Wed, Oct 26, 2005 at 01:14:28PM -0400, Jim Kress ccl_nospam]![kressworks.com wrote: > > Sent to CCL by: "Jim Kress" [ccl_nospam%kressworks.com] > Is there any way to set up a subscriber defined CCL filter to screen out all > the requests for help on Gaussian products? In the face of Gaussian's > refusal to provide adequate support of the products (developed with taxpayer > money) they sell (at exorbitant prices), I am sick and tired of repeatedly > having to manually delete each and every plea for help from frustrated > Gaussian users. I do not think this is the answer. Some requests raise some real issues. I agree that, generally (I get good responses direct from Gaussian), support is less than adequate and I was appalled at the increase in cost, for upgrading, with G03. If you do not like Gaussian, do not buy it. Let the market speak. Recently, I tried to find access to G03 to test whether a new link I had written in G98 still worked in G03. I found that virtually no department in Melbourne had purchased it. They all get grants to use it on the supercomputer cluster at a national facility. That is what I did. As an emeritus chemist, I certainly can not afford it. Brian. > Any help would be appreciated. > > Regards, > > Jim Kress > > "The reformation was preceded by the discovery of America, as if the > Almighty graciously meant to open a sanctuary to the persecuted in future > years, when home should afford neither friendship nor safety." -- Thomas > Paine (Common Sense, 1776) > -- Brian Salter-Duke (Brian Duke) b_duke|octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher, Chem., Melbourne Univ. & Med. Chem., Monash Univ. From owner-chemistry@ccl.net Wed Oct 26 22:56:01 2005 From: "Perry E. Metzger perry(a)piermont.com" To: CCL Subject: CCL:G: Filters Message-Id: <-29769-051026224820-11462-Yg9fpY1MJl5eta30SqNE9g{}server.ccl.net> X-Original-From: "Perry E. Metzger" Content-Type: text/plain; charset=us-ascii Date: Wed, 26 Oct 2005 22:48:16 -0400 MIME-Version: 1.0 Sent to CCL by: "Perry E. Metzger" [perry]|[piermont.com] "N. Sukumar" writes: > >the requests for help on Gaussian products? In the face of Gaussian's > >refusal to provide adequate support of the products (developed with taxpayer > >money) they sell (at exorbitant prices), I am sick and tired of repeatedly > >having to manually delete each and every plea for help from frustrated > >Gaussian users. > It should be a trivial matter to do this in whichever mail utility you > use. Many Gaussian questions posted here are from those who WILL not > read a manual, but many are useful to others; and if by "taxpayer > money" you refer to the program's origins at a public university, the > same could be said of almost every popular computational chemistry > program, most search engines and, if you include other sources of > taxpayer funds, even electronic computers and the internet itself. BSD Unix, which was created with taxpayer funds and was used as a TCP/IP testbed for many years, is fully open source. BIND, the most widely used DNS server on the internet, is open source. In fact, most of the technologies associated with the Internet are open. The underlying protocol specifications are available for free (as in freedom, not just as in money) download (unlike, say, ISO specs.) Most of the reference implementation work is open source. Most of the interesting code that makes the net interest these days -- everything from Apache to Perl to OpenSSL -- is open source. Much of the infrastructure that people use to keep the net running -- everything from SSH to Expect to Postfix to Snort -- is open source. Much computational chemistry code, written with taxpayer dollars, is not open source. One wonders why. Perry