From chemistry-request@server.ccl.net Fri Sep 20 16:09:42 2002 Received: from zeta.qmw.ac.uk ([138.37.6.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8KK9fw11110 for ; Fri, 20 Sep 2002 16:09:42 -0400 Received: from smtp.qmul.ac.uk ([138.37.6.40]) by zeta.qmw.ac.uk with esmtp (Exim 3.32 #1) id 17sU5q-0001rS-00 for CHEMISTRY@ccl.net; Fri, 20 Sep 2002 21:09:38 +0100 Received: from debye.chem.qmw.ac.uk ([138.37.52.177] helo=qmul.ac.uk) by smtp.qmul.ac.uk with esmtp (Exim 3.35 #5) id 17sU5r-0001eQ-00 for CHEMISTRY@ccl.net; Fri, 20 Sep 2002 21:09:39 +0100 Sender: pascal@ccl.net Message-ID: <3D8B8084.1747CA92@qmul.ac.uk> Date: Fri, 20 Sep 2002 21:09:40 +0100 From: Pascal Boulet Organization: Queen Mary, University of London X-Mailer: Mozilla 4.79C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: Dreiding parameters for Li and K Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I'd like to use the Dreiding force field to model the interactions of the Li and K ions with some molecules. Unfortunately I couldn't find the van der Waals parameters for these ions. Does anyone know where I could find these parameters? Thanks in advance, Pascal -- Dr. Pascal Boulet Queen Mary, University of London Centre for Computational Science Department of Chemistry Mile End Road London, E1 4NS UK Phone: (+44) (0)20 7882 7759 fax: (+44) (0)20 7882 7794 From chemistry-request@server.ccl.net Wed Sep 18 17:48:47 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8ILmlw31077 for ; Wed, 18 Sep 2002 17:48:47 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id RAA00171; Wed, 18 Sep 2002 17:36:47 -0400 (EDT) Date: Wed, 18 Sep 2002 17:36:47 -0400 From: Rick Venable To: Andrij Baumketner cc: chemistry@ccl.net Subject: Re: CCL:CHARMM: Is there any problem with velocity Verlet in c28b2 ? In-Reply-To: Message-ID: ReplyTo: Rick_Venable@nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I tried some tests with VVER at one point, with fairly unsatisfactory results-- plots of the total Hamiltonian vs. time (which should be flat) had fairly large fluctuations compared to extended system methods using the CPT keyword. It is possible to use the CPT keyword to do NVT ensemble MD; the trick is to set the pressure piston mass to zero, which fixes the volume and disables pressure-based coordinate scaling. In CHARMMspeak, dyna cpt restart nstep 50000 timestep 0.001 - pcons pint pref 1.0 pmass 0. - hoover reft 293.15 tmass 10000 - ... Note: CPT code requires the use of CRYStal for periodic boundary On Mon, 16 Sep 2002, Andrij Baumketner wrote: > I am trying to simulate a short peptide fully solvated in TIP3 water > by using 28beta2 version of CHARMM. I intend to employ constant NVT > conditions and, although the system under study is not particularly > large, I need a parallel implementation of the code. As far as I > understand, in CHARMM the NVT ensemble can only be generated in > parallel by using velocity version (VVER key) of the Verlet > algorithm combined with the Nose-Hoover thermostat. (I could > probably use CPT but I'm not sure about how scaling of coordinates > is dealt with there). When running a short simulation on a fully > equilibrated system I find that: > > a) VVER version produces considerably lower potential energy than > the original Verlet (non-parallel) algorithm when the SHAKE is > applied. The non-parallel Verlet gives results consistent with the > CPT ensemble simulations. > > b) if SHAKE is not applied the VVER algorithm just goes unstable. It > pumps all the energy into vibrations of both solute and solvent > molecules until the algorithm breaks. The original Verlet works just > fine under the same conditions. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Thu Sep 19 12:39:13 2002 Received: from copland.udel.edu ([128.175.13.92]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8JGdDw28070 for ; Thu, 19 Sep 2002 12:39:13 -0400 Received: from [128.175.138.90] ([128.175.138.90]) by copland.udel.edu (8.9.3/8.9.3) with ESMTP id MAA12920 for ; Thu, 19 Sep 2002 12:39:13 -0400 (EDT) Message-Id: <200209191639.MAA12920@copland.udel.edu> X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Date: Thu, 19 Sep 2002 12:18:34 -0400 Subject: summary on IR-spectra from G98 outputs From: "Olga Dmitrenko" To: chemistry@ccl.net Mime-version: 1.0 X-Priority: 3 Content-type: multipart/alternative; boundary="MS_Mac_OE_3115282714_379586_MIME_Part" > 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. --MS_Mac_OE_3115282714_379586_MIME_Part Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Dear CCLers, I would like to thank again Atte Sillanpaa , Roma E. Oakes, Laurence Cuffe and Jens Spanget-Larsen for their responses to my question. My best wishes to you. Yes, I agree with David Anick, that the answers have to be summarized, since it is quite general technical question that may be of interest for g98 users who do IR spectra calcs routinely. Here is the question again and, below, I've prepared a summary. Does anyone know the most time-economic way to convert frequency/intensity data from the g98 output file into 2-column data set for the IR-spectrum picture? Maybe some script exists for getting two columns: X=freqs and Y=IR Inten? 1) Roma E. Oakes: Roma E. Oakes Postgraduate Student School of Chemistry The Queen's University of Belfast David Keir Building Stranmillis Rd Belfast BT9 5AG Tel: (+)44 (0)28 91821021 Email: r.oakes@qub.ac.uk Home Page - http://home.btconnect.com/reoakes Roma E. Oakes has written a series of macros to tackle this, they work in excel and although you still have to press a few keys and manually change one number in the macro itself - they do save a huge amount of time. The good thing about them is that they will work for any molecule size 2) from Laurence Cuffe Laurence Cuffe is using Excel in the way described below: You may well be doing this already but this is what I do and it takes me about 5 minuets per file assuming the log file is called Job1.log grep Frequencies Job1.log > Job1F.txt grep Inten Job1.log >> Job1F.txt This gives me a text file Job1F.txt with the both the intensity and frequency data from Job1.log in it. import Job1F.txt into excell using the space character as your column separator cut at the start of the intensities section and paste the intensity information along side the frequency information I then insert a row at the top and label the data as CF1 CF2 CF3 CI1 CI2 CI3 I now have three columns of frequencies and three columns of intensities, appropriately labelled. I then use insert column to insert a column along side each of the frequency columns then cut and paste the intensity columns along side the corresponding frequency column. I then cut and paste the CF2 CI2 pair of columns onto the bottom of the CF1 CI1 pair and do the same for CF3 and CI3 (The column labels were just to keep track of where everything goes in this exercise) And then finally select both columns and do a data sort on frequency to get them all in order again. If you molecules were all the same size you could record a macro for this, but that's unlikely to be the case. 3) from JENS SPANGET-LARSEN : =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Jens Spanget-Larsen uses a small home-made BASIC program for this purpose. It reads the HyperChem script-file FREQCHK.SCR produced by the Gaussian utility FreqChk.exe (part of the Gaussian package) and creates two new files: one file with the X,Y-data you are looking for, and another file with data points for a Lorentz line plot. 1) Atte Sillanpaa atte.sillanpaa@oulu.fi +358 (0)8 553 1681 (work), KE 368 Dept. of Physical Chemistry +358 (0)40 592 7369 (gsm) Po-BOX 3000 FIN-90014 University of Oulu FINLAND | Entropy requires no maintenance. | Atte Sillanpaa wrote a very simple fortran program that reads in the lines containing the frequency and intensity, and then prints them in another file side by side. --MS_Mac_OE_3115282714_379586_MIME_Part Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable summary on IR-spectra from G98 outputs Dear CCLers,

I would like to thank again Atte Sillanpaa ,
Roma E. Oakes, Laurence Cuffe and Jens Spanget-Larsen  for their
responses to my question.  My best wishes to you.

Yes, I agree with David Anick, that the answers have to be summarized, sinc= e
it is quite general technical question that may be of interest for g98 user= s
who do IR spectra calcs routinely.

Here is the question again and, below, I've prepared a summary.

            &nb= sp;            &= nbsp;Does anyone know the most time-economic way to convert frequency/intens= ity
            &nb= sp;            &= nbsp;data from the g98 output file into 2-column data set for the IR-spectru= m picture?
            &nb= sp;            &= nbsp;Maybe some script exists for getting two columns: X=3Dfreqs and Y=3DIR Inte= n?
            &nb= sp;            &= nbsp;




1) Roma E. Oakes:
Roma E. Oakes
Postgraduate Student
School of Chemistry
The Queen's University of Belfast
David Keir Building
Stranmillis Rd
Belfast BT9 5AG
Tel: (+)44 (0)28 91821021
Email: r.oakes@qub.ac.uk
Home Page - http://home.btconnect.com/r= eoakes

Roma E. Oakes has written a series of macros to tackle this, the= y work in excel and
although you still have to press a few keys and manually change one number<= BR> in the macro itself - they do save a huge amount of time. The good thing about them is that they will work for any molecule size



2) from  Laurence Cuffe <Laurence.Cuffe@ucd.ie>

Laurence Cuffe is using Excel in the way described below:

You may well be doing this already but this is what I do and it
takes me about 5 minuets per file assuming the log file is called
Job1.log
grep Frequencies Job1.log > Job1F.txt
grep Inten Job1.log >> Job1F.txt
This gives me a text file Job1F.txt with the both the intensity and
frequency data from Job1.log in it.
import Job1F.txt into excell using the space character as your
column separator
cut at the start of the intensities section and paste the intensity
information along side the frequency information
I then insert a row at the top and label the data as
CF1 CF2 CF3 CI1 CI2 CI3
I now have three columns of frequencies and three columns of
intensities, appropriately labelled.  I then use insert column to
insert a column along side each of the frequency columns then cut
and paste the intensity columns along side the corresponding
frequency column.
I then cut and paste the CF2 CI2 pair of columns onto the bottom
of the CF1 CI1 pair and do the same for CF3 and CI3 (The column
labels were just to keep track of where everything goes in this
exercise)
And then finally select both columns and do a data sort on
frequency to get them all in order again.
If you molecules were all the same size you could record a macro
for this, but that's unlikely to be the case.

3) from JENS SPANGET-LARSEN :
=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
JENS SPANGET-LARSEN         Office:=         +45 4674 2710
Department of Chemistry     Fax:    &nbs= p;       +45 4674 3011
Roskilde University (RUC)   Mobile:      = ;   +45 2320 6246
P.O.Box 260           &nb= sp;     E-Mail:       = ; spanget@ruc.dk
DK-4000 Roskilde, Denmark   h= ttp://virgil.ruc.dk/~spanget
=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

Jens Spanget-Larsen uses a small home-made BASIC program for this = purpose.
It reads the HyperChem script-file FREQCHK.SCR produced by the Gaussian uti= lity
FreqChk.exe (part of the Gaussian package) and creates two new files:
one file with the X,Y-data you are looking for, and another file with
data points for a Lorentz line plot.

1)  Atte Sillanpaa

 atte.sillanpaa@oulu.fi &= nbsp;+358 (0)8 553 1681 (work), KE 368
 Dept. of Physical Chemistry +358 (0)40 592 7369 (gsm)
 Po-BOX 3000
 FIN-90014 University of Oulu
 FINLAND
            &nb= sp;     |   Entropy requires no maintenan= ce.   |

Atte Sillanpaa wrote a very simple fortran program that reads
in the lines containing the frequency and intensity, and then prints
them in another file side by side.


 --MS_Mac_OE_3115282714_379586_MIME_Part-- From chemistry-request@server.ccl.net Fri Sep 20 13:53:20 2002 Received: from rwcrmhc51.attbi.com ([204.127.198.38]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8KHrKw06921 for ; Fri, 20 Sep 2002 13:53:20 -0400 Received: from C1353359A ([12.228.187.234]) by rwcrmhc51.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with SMTP id <20020920175315.FUQB21615.rwcrmhc51.attbi.com@C1353359A>; Fri, 20 Sep 2002 17:53:15 +0000 Reply-To: From: "Mark Thompson" To: Cc: Subject: FW: Onsager equation Date: Fri, 20 Sep 2002 10:51:38 -0700 Message-ID: <000101c260ce$5e7c5050$0300a8c0@attbi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Importance: Normal Andy, Here is a good journal article that gives one approach to what you are looking for: Karelson and Zerner, J. Phys. Chem. vol 96, 6949-6957, (1992) Mark ================================= Mark Thompson, Ph.D. Planaria Software PO Box 55207 Seattle, WA 98155 http://www.arguslab.com FAX: 206-440-3305 ================================= > > > -----Original Message----- > > From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On > > Behalf Of Ng Man Fai > > Sent: Wednesday, September 18, 2002 2:44 AM > > To: CHEMISTRY@ccl.net > > Subject: CCL:Onsager equation > > > > > > Hi, may I ask that how to implement the Onsager equation for calculating > > the solvent effect in the excited state calculations? I have changed the > > ground state fock matrix by adding the dielectric term, but where to put > > the index of refraction term? > > > > Best regards, > > Andy > > > >