From owner-chemistry@ccl.net Fri Oct 26 05:45:01 2007
From: "Joe Kwiatkowski jk905-*-imperial.ac.uk" <owner-chemistry]^[server.ccl.net>
To: CCL
Subject: CCL:G: 6-31+g* orbitals!=basis functions
Message-Id: <-35489-071025132033-6244-gTFjY/jBE/pKXL9RFB0YNA]^[server.ccl.net>
X-Original-From: Joe Kwiatkowski <jk905,+,imperial.ac.uk>
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Date: Thu, 25 Oct 2007 17:37:34 +0100
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Sent to CCL by: Joe Kwiatkowski [jk905(_)imperial.ac.uk]
Dear CCL'ers
I have been running B3LYP/6-31+G* calculations on Naphthalene with G03.
I am confused because the number of basis functions is 206, but
'punch=MO' only returns 205 orbitals. If I request the overlap matrix
with iop(3/33=1) I see all 206 orbitals.
What is going on? Any ideas?
With thanks in advance,
Joe
--
Joe Kwiatkowski
EXSS, Physics
Imperial College London
Prince Consort Road
SW7 2BW
Tel: 0207 594 6682
From owner-chemistry@ccl.net Fri Oct 26 05:59:01 2007
From: "alexandra.marques===fc.up.pt" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL:G: amber torsions
Message-Id: <-35490-071025235027-583-s0KHZ63EKQ8rMdpmY9Yfpg(0)server.ccl.net>
X-Original-From: alexandra.marques*|*fc.up.pt
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Date: Fri, 26 Oct 2007 04:49:57 +0200
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Sent to CCL by: alexandra.marques%x%fc.up.pt
Hi
I am a little bit confused about the way to specify amber torsions for =20
use with the amber (softfirst) in a oniom calculation in gaussian.
In manual it is said that the amber torsions are specified this way:
AmbTrs Atom-type1 A-type2 A-type3 A-type4 PO1 PO2 PO3 PO4 Mag1 Mag2 =20
Mag3 Mag4 NPaths
PO1-PO4 Phase offsets
Mag1...Mag4 V/2 magnitudes
NPaths Number of paths (if < 0, determined on-the-fly).
So for isntance, if I have the following parameters for a dihedral =20
CX-CY-CC-CZ:
CX-CY-CC-CZ 1 0.850 180 -3
CX-CY-CC-CZ 1 0.940 180 -2
CX-CY-CC-CZ 1 -0.560 180 1
the way to specify this in amber is:
AmbTrs CX CY CC CZ 180 180 180 0.850 0.940 -0.560 1 1 1
Is this correct?
When using amber in gaussian, is it necessary to always specify the =20
torsion parameters involving new atom types or we just need to specify =20
the bond and angle parameters?
Thanks
Alexandra
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From owner-chemistry@ccl.net Fri Oct 26 08:43:00 2007
From: "Simon Halstead joyjoyhappyjoy * yahoo.co.uk" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL: MD of systems with a net charge using Ewald
Message-Id: <-35491-071025232859-31466-QAfQONfEGdhTx1zgaDzgNQ : server.ccl.net>
X-Original-From: "Simon Halstead" <joyjoyhappyjoy#,#yahoo.co.uk>
Date: Thu, 25 Oct 2007 23:28:56 -0400
Sent to CCL by: "Simon Halstead" [joyjoyhappyjoy(a)yahoo.co.uk]
Dear all,
I am running MD simulations on systems with either a net +1 or -1 charge using Ewald summation and dl_poly. The Ewald summation should correct for the net charge by adding a smeared charge over the cell. However, my results show a serious system size dependence for the potential energy (from the coulomb term).
Does anyone know of any way to correct the energy results?
Amy help would be greatly appreciated,
Simon
From owner-chemistry@ccl.net Fri Oct 26 10:52:00 2007
From: "Jinyao Wang wangjy::ciac.jl.cn" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL: help me
Message-Id: <-35492-071026104742-24784-iNIp5ioffPjwO3lCiVzB6Q##server.ccl.net>
X-Original-From: "Jinyao Wang" <wangjy*o*ciac.jl.cn>
Date: Fri, 26 Oct 2007 10:47:39 -0400
Sent to CCL by: "Jinyao Wang" [wangjy[a]ciac.jl.cn]
Dear CCL'er,
I am trying to optimize different geometries between acetaldehyde and carbon dioxide moleculars in differernt pressures of CO2 when acetaldehyde dissolve into CO2. So I want to find some available softwares to perform it.
I would appreciate if you could give me some suggestions.
From owner-chemistry@ccl.net Fri Oct 26 11:26:01 2007
From: "immanuel feng feng.immanuel-$-gmail.com" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL: problem with nwchem 5.0
Message-Id: <-35493-071025115014-15111-3hQ1sqbLGWEkS64JajNzDQ(!)server.ccl.net>
X-Original-From: "immanuel feng" <feng.immanuel-$-gmail.com>
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Date: Thu, 25 Oct 2007 22:46:24 +0800
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Sent to CCL by: "immanuel feng" [feng.immanuel===gmail.com]
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hello everyone,
I am pretty new to nwchem, now I want to perform the single point
energy calculation with M05 DFT method on nwchem. My input file is below,
but it said the dft_input directive is unknown. Could anyone give me some
advice? Thank you so much!
yesu
start try
charge 0
geometry
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.094223
H 1.031641 0.000000 -0.364776
H -0.515826 -0.893440 -0.364756
H -0.515854 0.893405 -0.364787
end
basis
* library 6-311++g(3df,3pd)
end
dft
m05; singlet
print low
end
task dft
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<div>hello everyone, </div>
<div> I am pretty new to nwchem, now I =
want to perform the single point energy calculation with M05 DFT method on =
nwchem. My input file is below, but it said the dft_input directive is unkn=
own. Could anyone give me some advice? Thank you so much!
</div>
<div> </div>
<div> &nbs=
p; &=
nbsp; &nbs=
p; &=
nbsp; &nbs=
p; &=
nbsp; &nbs=
p; &=
nbsp; &nbs=
p; &=
nbsp; &nbs=
p; &=
nbsp; &nbs=
p; &=
nbsp; &nbs=
p; &=
nbsp; &nbs=
p; &=
nbsp; yesu
</div>
<div> </div>
<div>start try<br> <br>charge 0<br> <br>geometry<br> C =
0.000000 0.000000 &nb=
sp; 0.000000<br> H 0.000000 &=
nbsp; 0.000000 1.094223<br> H  =
; 1.031641 0.000000 -=
0.364776<br> H -0.515826 -0.893440=
-
0.364756<br> H -0.515854 0.8=
93405 -0.364787<br>end<br> <br>basis<br>* library 6-=
311++g(3df,3pd)<br>end<br> <br>dft<br> m05; singlet<br> prin=
t low<br>end<br> <br>task dft</div>
------=_Part_895_376303.1193323584918--
From owner-chemistry@ccl.net Fri Oct 26 12:07:01 2007
From: "Konrad Hinsen hinsen+/-cnrs-orleans.fr" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: MD of systems with a net charge using Ewald
Message-Id: <-35494-071026112256-6435-SseN4GkQA55D6nP67Fc5nw[*]server.ccl.net>
X-Original-From: "Konrad Hinsen" <hinsen||cnrs-orleans.fr>
Date: Fri, 26 Oct 2007 11:22:53 -0400
Sent to CCL by: "Konrad Hinsen" [hinsen#cnrs-orleans.fr]
On Oct 26, 2007, at 5:28, Simon Halstead joyjoyhappyjoy * yahoo.co.uk wrote:
> I am running MD simulations on systems with either a net +1 or -1 charge using Ewald summation
> and dl_poly. The Ewald summation should correct for the net charge by adding a smeared charge
> over the cell. However, my results show a serious system size dependence for the potential energy
> (from the coulomb term).
> Does anyone know of any way to correct the energy results?
Ewald summation does indeed add a neutralizing background charge density, which makes the
electrostatic energy finite. However, the energy depends on the system size. If you think that in your
specific case the energy should not depend on system size, then please tell us why.
--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Molculaire, CNRS Orlans
Synchrotron Soleil - Division Expriences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen^_^cnrs-orleans.fr
---------------------------------------------------------------------
From owner-chemistry@ccl.net Fri Oct 26 12:51:01 2007
From: "Aleksandra Rudnitskaya aleksandra.rudnit001-x-umb.edu" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL:G: G03 problem with readisotopes
Message-Id: <-35495-071025204841-21806-mfz0FcwEvghhJ6438YYXrw---server.ccl.net>
X-Original-From: "Aleksandra Rudnitskaya" <aleksandra.rudnit001#,#umb.edu>
Date: Thu, 25 Oct 2007 20:48:37 -0400
Sent to CCL by: "Aleksandra Rudnitskaya" [aleksandra.rudnit001===umb.edu]
Dear CCLers,
I wanted to calculate opt and freq on water with different temperature and pressure. Input file looks following
%Chk=h2o_t2
# opt freq=noraman rb3lyp/6-311++g(3df,3pd)
Title
0 1
O
H 1 B1
H 1 B2 2 A1
B1 0.960000
B2 0.960000
A1 109.471221
--Link1--
%chk=h2o_t2
# rb3lyp/6-311++g(3df,3pd) freq=(readfc,readisotopes) Geom=AllCheck
400.0 1.0
The error message is
# rb3lyp/6-311++g(3df,3pd) freq=(readfc,readisotopes) Geom=AllCheck
-------------------------------------------------------------------
1/29=7,38=1,88=2/1;
2/40=1/2;
7/8=1,25=11/16;
99/5=2,8=2/99;
-----
Title
-----
Redundant internal coordinates taken from checkpoint file:
h2o_t2.chk
Charge = 0 Multiplicity = 1
O,0,-0.0165597067,0.,-0.0117094809
H,0,0.0205206193,0.,0.9485436833
H,0,0.9011357673,0.,-0.2968342024
Recover connectivity data from disk.
WANTED A FLOATING POINT NUMBER AS INPUT.
FOUND A STRING AS INPUT.
Atom number 2, atomic number 1: [1]
?
Error termination via Lnk1e in /usr/apps/chemistry/gaussian/G03/nbo/g03/l101.exe at Tue
Oct 23 18:37:35 2007.
Job cpu time: 0 days 0 hours 0 minutes 0.3 seconds.
File lengths (MBytes): RWF= 13 Int= 0 D2E= 0 Chk= 10 Scr= 1
It seams G03( unix cluster) doesnt like temperature and pressure, while the same file was done on G98 (windows) . Any suggestions? how to fix it? Thanks in advance.
Aleksandra
From owner-chemistry@ccl.net Fri Oct 26 13:33:00 2007
From: "Jeff Hammond jeff.science**gmail.com" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL: problem with nwchem 5.0
Message-Id: <-35496-071026120935-6583-mDvFBOEXVmT5zj6uaZrJJg_._server.ccl.net>
X-Original-From: "Jeff Hammond" <jeff.science===gmail.com>
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Date: Fri, 26 Oct 2007 11:09:24 -0500
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Sent to CCL by: "Jeff Hammond" [jeff.science() gmail.com]
Immanuel,
Please modify the dft input block as follows:
dft
xc m05
print low
end
The singlet command is not understood in the DFT input block. In this
case it is unnecessary, but you can add it to the SCF block like this:
scf
singlet
end
Section 11 of the NWChem User Manual
(http://www.emsl.pnl.gov/docs/nwchem/doc/user/user.html) covers DFT.
You can also find a number of examples in the $NWCHEM_TOP/QA/tests.
If you may eventually want to use the m06 functions, please go here to
get the necessary patch:
http://www.emsl.pnl.gov/docs/nwchem/support/faq/m06.html
In the future, please post questions about NWChem to
nwchem-users#emsl.pnl.gov. You'll get better answers faster.
Jeff
From owner-chemistry@ccl.net Fri Oct 26 16:07:00 2007
From: "Jerome Kieffer jerome.Kieffer[A]terre-adelie.org" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL: Geometry optimization software ?
Message-Id: <-35497-071026160139-1983-Y1mcJdjh87nID/ukXR2+og=server.ccl.net>
X-Original-From: Jerome Kieffer <jerome.Kieffer---terre-adelie.org>
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Date: Fri, 26 Oct 2007 22:03:58 +0200
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Sent to CCL by: Jerome Kieffer [jerome.Kieffer(a)terre-adelie.org]
On Thu, 25 Oct 2007 16:35:38 +0900
"Yangsoo Kim vsmember_+_gmail.com" <owner-chemistry:-:ccl.net> wrote:
> I would greatly appreciate if you could drop me a line with the name of
> software showing good performance for the global geometry optimization.
I am using the ConFlex code (provided in the CAChe worksuite) to
generate a set of conformers before re-optimizing each of them using
DFT or semi-empirical methods.
Hopt this helps.
--=20
J=E9r=F4me KIEFFER : http://www.terre-adelie.org