From owner-chemistry@ccl.net Wed Dec 17 03:27:00 2008
From: "Mahmoud Korani Abdel-Latif mkkhedr*_*hotmail.com" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL: CPMD MD run Zero Usage of the CPU
Message-Id: <-38316-081217032533-23591-s0kGHJ+EP7T8BWxHKdgXlQ _ server.ccl.net>
X-Original-From: "Mahmoud Korani Abdel-Latif" <mkkhedr*hotmail.com>
Date: Wed, 17 Dec 2008 03:25:29 -0500


Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr(!)hotmail.com]
Dear CCLers,

I am doing MD for molecular crystals using CPMD package in parallel and the problem is that, after certain number of steps I found zero usage of the cpmd program and there is no any new lines added in the output files. This occurred without any exit of the program.

Also the Cell parameter I am using is for monoclinic crystal but I have seen in the output file the type of the crystal is triclinic one.

The space group symmetry of that crystal is p21/c, and this type is not available in the symmetry groups which in the CPMD manual.

Is it any keyword to deal the crystals?

Any help should be appreciated.

Best Regards,
Mahmoud


From owner-chemistry@ccl.net Wed Dec 17 04:38:00 2008
From: "Ol Ga eurisco1]-[pochta.ru" <owner-chemistry-.-server.ccl.net>
To: CCL
Subject: CCL: CPMD MD run Zero Usage of the CPU
Message-Id: <-38317-081217043159-21760-0a0KgP9izcdPkNvSEiDMhg-.-server.ccl.net>
X-Original-From: "Ol  Ga" <eurisco1/./pochta.ru>
Date: Wed, 17 Dec 2008 04:31:55 -0500


Sent to CCL by: "Ol  Ga" [eurisco1[#]pochta.ru]
Dear Mahmoud Korani Abdel-Latif,

 I suggest you to forward your question direct to the CPMD developers and user list

>CPMD consortium mailing list
This is the driver to the cpmd mailing list. The list is managed using mailman and should be used to exchange information in the cpmd community, e.g.software problems, new ideas, bug reports. The list is digested, so that >only proper mail will be forwarded .

http://www.cpmd.org/cpmd_mailinglist.html


Sincerely,

Ol Ga


> Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr(!)hotmail.com]
> Dear CCLers,

> I am doing MD for molecular crystals using CPMD package in parallel
> and the problem is that, after certain number of steps I found zero
> usage of the cpmd program and there is no any new lines added in the
> output files. This occurred without any exit of the program.

> Also the Cell parameter I am using is for monoclinic crystal but I
> have seen in the output file the type of the crystal is triclinic one.

> The space group symmetry of that crystal is p21/c, and this type is
> not available in the symmetry groups which in the CPMD manual.

> Is it any keyword to deal the crystals?

> Any help should be appreciated.

> Best Regards,
> Mahmoud


From owner-chemistry@ccl.net Wed Dec 17 07:03:00 2008
From: "Andreas Klamt klamt%a%cosmologic.de" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: translational entropy and solvation
Message-Id: <-38318-081217065954-31395-0JCig4MW94ZBbZC5m6SY/g**server.ccl.net>
X-Original-From: Andreas Klamt <klamt]_[cosmologic.de>
Content-Transfer-Encoding: 7bit
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Date: Wed, 17 Dec 2008 12:59:36 +0100
MIME-Version: 1.0


Sent to CCL by: Andreas Klamt [klamt\a/cosmologic.de]
Just a short reply:
- I personly am not that happy that the cell method always is applied to 
aqueous systems. Here we have strong contributions to enthalpy and 
entropy for the formation of hydrogen bonds, ... Would your method also 
apply for a cylohexane? If yes, what are the results?
- I am confused by your statement that the solute reduces the entropy of 
the solvent by the excluded volume: As far as I can see solvation is 
usually considered at constant pressure, not at constant volume. It is 
assumed that the solvent can get the missing volume elsewhere.
- And I am not happy that you agree with my regarding the 3/2 vs. 5/2 RT 
for the translational entropy of a molecule in the gasphase: Meanwhile 
Frank Jensen told me that his erratum was wrong and that is should be 
5/2, and he sent me a plausible derivation of that. The Atkins book also 
says 5/2. When you look to the internet you find 3/2 and 5/2 about 
equally often, and you find nice derivations for both. I am completely 
confused now and have to clarify this for myself over Christmas. Is 
there a difference in the ensembles considered? I do not find that in 
the premisses of the literature derivations.
- I admit that I did not take into account that in a classical ensemble 
the reduction of the kinetic energy would correspond to a temperature 
decrease. I myself am not sure about the degree of quantum effects here. 
Anyway, in a quantum system we cannot do the integrals for position and 
momentum separately and the discussion becomes useless.

I am afraid that at the end of the discussion we will have to admit that 
there is no way to define or to measure the translational entropy of a 
solute in solution. I only can say that empirically we find the 
described significant free energy change of ~3 kcal/mol in the 
previously described A + A --> AA reaction, where all surface 
proportional, electrostatic, and hydrogen bonding interactions of AA are 
just twice those of A.

Best regards

Andreas


> Sent to CCL by: "Richard  Henchman" [henchman,manchester.ac.uk]
> It is possible to regard a solute as having the ideal-gas entropy in
> solution, but it is not the only possibility because there is no
> unique way to allocate entropy to each molecule in the solution, as
> Raphael Ribeiro (9 Dec) and Mike Gilson (11 Dec) have already pointed
> out.
>
> This can be made clear by considering the example of water dissolved
> in water (use D2O if you prefer to have labels and ignoring the fact
> that it would form HOD). If you assign this solute water the ideal-gas
> entropy (~129 J/K/mol at 298 K for water at the density of liquid
> water), then the entropy of the surrounding water molecules is reduced
> due to excluded volume by the solute, as is the common practice. This
> ensures that the total entropy of the solution equals that of bulk
> water. Another possibility is to give the solute water molecule the
> same entropy of all the other water molecules i.e. less than the gas
> phase (~70 J/K/mol at 298 K). How one could calculate such an entropy
> I have shown in some recent publications on water:
> http://link.aip.org/link/?JCP/126/064504 and a quantised version
> http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/2008/112/i32/abs/jp0737303.html
>
> These same ideas would apply to any solute, not just a solute water
> molecule. The solute would have lower entropy than the ideas-gas value
> due to confinement by the solvent. The solute takes all possible
> positions and orientations but its freedom is still constrained by
> where the other solvent molecules are. If this seems
> counter-intuitive, it is only because the dimensionality of 3N-space is
> so large. One could even consider a case intermediate between the
> confined solute and the ideal-gas solute. In any case, whichever
> solution model one uses, the solute and solvent entropy must add up to
> give the total entropy of the solution. I think a number of
> contributors to this discussion are right to question whether current
> solvation models do this.
>
> A few other comments: Andreas Klamt is correct to emphasise that the
> ideal-gas entropy should be 3k/2 and not 5k/2 because the entropy
> relates to a single molecule. However, I am not convinced by the
> statement that "the solvent definitely reduces the motional (kinetic)
> phase space". That amounts to saying that the solvent is at a lower
> temperature. Ignoring quantum effects, which I believe to be small
> (based on my second publication given above), the momentum partition
> functions should be very similar.
>
> Richard Henchman
>
>
> __
> Dr Richard H Henchman
> The University of Manchester
> http://personalpages.manchester.ac.uk/staff/henchman/
>   


-- 
--------------------------------------------------------------------------
Dr. habil. Andreas Klamt
COSMOlogic GmbH&CoKG
Burscheider Str. 515
51381 Leverkusen, Germany

Tel.: +49-2171-73168-1  Fax:  +49-2171-73168-9
e-mail: klamt]-[cosmologic.de
web:    www.cosmologic.de
--------------------------------------------------------------------------
COSMOlogic
       Your Competent Partner for
       Computational Chemistry and Fluid Thermodynamics
--------------------------------------------------------------------------
Please note our COSMO-RS Symposium in 2009 
(For details see: http://www.cosmologic.de/Symposium/symposium.html)


From owner-chemistry@ccl.net Wed Dec 17 07:47:01 2008
From: "Leyla Ramin l.ramin(a)aeromech.usyd.edu.au" <owner-chemistry~~server.ccl.net>
To: CCL
Subject: CCL: CPMD MD run Zero Usage of the CPU
Message-Id: <-38319-081217074604-2983-0JCig4MW94ZBbZC5m6SY/g~~server.ccl.net>
X-Original-From: "Leyla Ramin" <l.ramin^-^aeromech.usyd.edu.au>
Content-class: urn:content-classes:message
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Sent to CCL by: "Leyla Ramin" [l.ramin+/-aeromech.usyd.edu.au]
This is a multi-part message in MIME format.

------_=_NextPart_001_01C96045.63D9AF8D
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Hi,
I am doing MD for simple lennard jones forces, I faced with the problem =
that when I apply Lennard jones, the atomes sometimes get too close too =
each other and the forces goes to infinity, How can I manage this =
problem.=20
=20
Kind Regards
Leyla Ramin

________________________________

> From: owner-chemistry+lram5228=3D=3Dusyd.edu.au^^ccl.net on behalf of =
Mahmoud Korani Abdel-Latif mkkhedr*_*hotmail.com
Sent: Wed 17/12/2008 19:25
To: Leyla Ramin
Subject: CCL: CPMD MD run Zero Usage of the CPU




Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr(!)hotmail.com]
Dear CCLers,

I am doing MD for molecular crystals using CPMD package in parallel and =
the problem is that, after certain number of steps I found zero usage of =
the cpmd program and there is no any new lines added in the output =
files. This occurred without any exit of the program.

Also the Cell parameter I am using is for monoclinic crystal but I have =
seen in the output file the type of the crystal is triclinic one.

The space group symmetry of that crystal is p21/c, and this type is not =
available in the symmetry groups which in the CPMD manual.

Is it any keyword to deal the crystals?

Any help should be appreciated.

Best Regards,
Mahmoud



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<HTML dir=3Dltr><HEAD><TITLE>CCL: CPMD MD run Zero Usage of the =
CPU</TITLE>=0A=
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<DIV dir=3Dltr><FONT face=3DArial color=3D#000000 =
size=3D2>Hi,</FONT></DIV>=0A=
<DIV dir=3Dltr><FONT face=3DArial size=3D2>I am doing MD for simple =
lennard jones forces, I faced with the problem that when I apply Lennard =
jones, the atomes sometimes get too close too each other&nbsp;and the =
forces goes to infinity, How can I manage this =
problem.&nbsp;</FONT></DIV>=0A=
<DIV dir=3Dltr><FONT face=3DArial color=3D#000000 =
size=3D2></FONT>&nbsp;</DIV></DIV>=0A=
<DIV id=3DidSignature96255 dir=3Dltr><PRE>Kind Regards=0A=
Leyla Ramin</PRE></DIV>=0A=
<DIV dir=3Dltr><BR>=0A=
<HR tabIndex=3D-1>=0A=
<FONT face=3DTahoma size=3D2><B>From:</B> =
owner-chemistry+lram5228=3D=3Dusyd.edu.au^^ccl.net on behalf of Mahmoud =
Korani Abdel-Latif mkkhedr*_*hotmail.com<BR><B>Sent:</B> Wed 17/12/2008 =
19:25<BR><B>To:</B> Leyla Ramin<BR><B>Subject:</B> CCL: CPMD MD run Zero =
Usage of the CPU<BR></FONT><BR></DIV>=0A=
<DIV><BR>=0A=
<P><FONT size=3D2>Sent to CCL by: "Mahmoud Korani Abdel-Latif" =
[mkkhedr(!)hotmail.com]<BR>Dear CCLers,<BR><BR>I am doing MD for =
molecular crystals using CPMD package in parallel and the problem is =
that, after certain number of steps I found zero usage of the cpmd =
program and there is no any new lines added in the output files. This =
occurred without any exit of the program.<BR><BR>Also the Cell parameter =
I am using is for monoclinic crystal but I have seen in the output file =
the type of the crystal is triclinic one.<BR><BR>The space group =
symmetry of that crystal is p21/c, and this type is not available in the =
symmetry groups which in the CPMD manual.<BR><BR>Is it any keyword to =
deal the crystals?<BR><BR>Any help should be appreciated.<BR><BR>Best =
Regards,<BR>Mahmoud<BR><BR><BR><BR>-=3D This is automatically added to =
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From owner-chemistry@ccl.net Wed Dec 17 08:22:01 2008
From: "Leila Ramin lram5228**usyd.edu.au" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL: Lennard jones
Message-Id: <-38320-081217075516-9846-Z3YsMKx9al9LrbT6vUfupQ,,server.ccl.net>
X-Original-From: "Leila  Ramin" <lram5228[A]usyd.edu.au>
Date: Wed, 17 Dec 2008 07:55:13 -0500


Sent to CCL by: "Leila  Ramin" [lram5228__usyd.edu.au]
Hi,
I am doing MD for simple Lennard jones forces, I faced with the problem that when I apply Lennard jones, the atomes sometimes get too close to each other and the forces increase to infinity, How can I manage this problem. 

Kind Regards
Leyla Ramin


From owner-chemistry@ccl.net Wed Dec 17 09:16:01 2008
From: "Ol Ga eurisco1(!)pochta.ru" <owner-chemistry\a/server.ccl.net>
To: CCL
Subject: CCL: To Leyla Ramin - about CPMD consortium mailing list
Message-Id: <-38321-081217091235-11817-9/BO6zVaZTSJV6IXPsFC1g\a/server.ccl.net>
X-Original-From: "Ol  Ga" <eurisco1{=}pochta.ru>
Date: Wed, 17 Dec 2008 09:12:31 -0500


Sent to CCL by: "Ol  Ga" [eurisco1 a pochta.ru]
Dear Leyla Ramin,

 I suggest you to forward your question _direct_ to the CPMD developers and user list

>CPMD consortium mailing list
This is the driver to the cpmd mailing list. The list is managed using mailman and should be used to exchange information
in the cpmd community, e.g.software problems, new ideas, bug reports. The list is digested, so that >only proper mail will
be forwarded .

http://www.cpmd.org/cpmd_mailinglist.html


Sincerely,

Ol Ga


> Hi,
> I am doing MD for simple lennard jones forces, I faced with the
> problem that when I apply Lennard jones, the atomes sometimes get
> too close too each other and the forces goes to infinity, How can I manage this problem.
>  
> Kind Regards
> Leyla Ramin


From owner-chemistry@ccl.net Wed Dec 17 09:50:00 2008
From: "Vincent Leroux vincent.leroux:loria.fr" <owner-chemistry:+:server.ccl.net>
To: CCL
Subject: CCL: Lennard jones
Message-Id: <-38322-081217090709-9252-B+j1FtkIGhX3cjhaUGldng:+:server.ccl.net>
X-Original-From: Vincent Leroux <vincent.leroux---loria.fr>
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Date: Wed, 17 Dec 2008 15:06:58 +0100
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Sent to CCL by: Vincent Leroux [vincent.leroux,+,loria.fr]
Hi Leyla,

1/ Check that your system have been correctly equilibrated.
2/ Make sure the simulation time step is not set too large.
3/ Apply constraints on bond lengths using SHAKE or the like.

VL


Leila Ramin lram5228**usyd.edu.au a écrit :
> Sent to CCL by: "Leila  Ramin" [lram5228__usyd.edu.au]
> Hi,
> I am doing MD for simple Lennard jones forces, I faced with the problem that when I apply Lennard jones, the atomes sometimes get too close to each other and the forces increase to infinity, How can I manage this problem. 
>
> Kind Regards
> Leyla Ramin
>
>
>


From owner-chemistry@ccl.net Wed Dec 17 11:16:00 2008
From: "Ramon Crehuet rcsqtc\a/iqac.csic.es" <owner-chemistry~!~server.ccl.net>
To: CCL
Subject: CCL: Lennard jones
Message-Id: <-38323-081217102607-28735-guSpzo9MIPyx28E3frj3Ow~!~server.ccl.net>
X-Original-From: Ramon Crehuet <rcsqtc{=}iqac.csic.es>
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Sent to CCL by: Ramon Crehuet [rcsqtc^-^iqac.csic.es]
Hy Leila,
Reduce the time-step. Check for energy conservation and don't use
thermostats (use NVE ensemble) to check the parameters are stable.
Regards,

Ramon



Leila Ramin lram5228**usyd.edu.au wrote:
> Sent to CCL by: "Leila  Ramin" [lram5228__usyd.edu.au]
> Hi,
> I am doing MD for simple Lennard jones forces, I faced with the problem that when I apply Lennard jones, the atomes sometimes get too close to each other and the forces increase to infinity, How can I manage this problem. 
> 
> Kind Regards
> Leyla Ramin> 
> 
>


From owner-chemistry@ccl.net Wed Dec 17 11:53:01 2008
From: "Mihaly Mezei Mihaly.Mezei : mssm.edu" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL: Lennard jones
Message-Id: <-38324-081217115005-32389-h6GbZ8AjmzIw6ZYiPq2vSQ]_[server.ccl.net>
X-Original-From: Mihaly Mezei <Mihaly.Mezei::mssm.edu>
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Date: Wed, 17 Dec 2008 11:49:51 -0500
MIME-version: 1.0


Sent to CCL by: Mihaly Mezei [Mihaly.Mezei(~)mssm.edu]
> Sent to CCL by: "Leila  Ramin" [lram5228__usyd.edu.au]
> Hi,
> I am doing MD for simple Lennard jones forces, I faced with the 
> problem that when I apply Lennard jones, the atomes sometimes get 
> too close to each other and the forces increase to infinity, How 
> can I manage this problem. 

Try minimizing fisrt the system and then warm it up in steps of , say, 10K.

Mihaly Mezei

Department of Structural and Chemical Biology, Mount Sinai School of Medicine, NYU
Voice:  (212) 659-5475   Fax: (212) 849-2456
WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632
WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
WWW (Department): http://atlas.physbio.mssm.edu

----- Original Message -----
> From: "Leila Ramin lram5228**usyd.edu.au" <owner-chemistry!=!ccl.net>
Date: Wednesday, December 17, 2008 7:55 am
Subject: CCL: Lennard jones

> 

> 
> Kind Regards
> Leyla Ramin
> 
> 
> 
> -= This is automatically added to each message by the mailing 
> script =-
> To recover the email address of the author of the message, please 
> changethe strange characters on the top line to the !=! sign. You can 
> also> Conferences: 
> http://server.ccl.net/chemistry/announcements/conferences/
> Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: 
> search)> 
> 
>


From owner-chemistry@ccl.net Wed Dec 17 12:28:00 2008
From: "John Gunn jgunn ~ mailaps.org" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: translational entropy and solvation
Message-Id: <-38325-081217105640-11707-XWXgvD4UZrdoGA5ohIEz0g:server.ccl.net>
X-Original-From: John Gunn <jgunn::mailaps.org>
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Sent to CCL by: John Gunn [jgunn=-=mailaps.org]
> - And I am not happy that you agree with my regarding the 3/2 vs. 5/2 RT 
> for the translational entropy of a molecule in the gasphase: Meanwhile 
> Frank Jensen told me that his erratum was wrong and that is should be 
> 5/2, and he sent me a plausible derivation of that. The Atkins book also 
> says 5/2. When you look to the internet you find 3/2 and 5/2 about 
> equally often, and you find nice derivations for both. I am completely 
> confused now and have to clarify this for myself over Christmas. Is 
> there a difference in the ensembles considered? I do not find that in 
> the premisses of the literature derivations.

The difference here is Gibbs paradox.  It depends on whether or not you
are considering distinguishable particles.

-- 
 John Gunn (jgunn*_*mailaps.org)  | "Ain't no Vietcong
 Chemical software development  |    ever called me nigger"
 Rosemere, Quebec               |     - Muhammad Ali (1964)


From owner-chemistry@ccl.net Wed Dec 17 13:03:00 2008
From: "moura]^[ufscar.br" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL: translational entropy and solvation
Message-Id: <-38326-081217114513-28265-0vQ6yv7Ss0c1s1uTl02vTQ^^server.ccl.net>
X-Original-From: moura%ufscar.br
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Date: Wed, 17 Dec 2008 14:08:30 -0200 (BRST)
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Sent to CCL by: moura.|a|.ufscar.br
Dear all,

I would just like to point out that it is experimentally found out that
molecules
in solution have a concentration dependent partial volume, meaning that in a
real solution, as opposed to an ideal one, there should be a different volume
available for each molecule, a volume that depends on the intermolecular
interactions but does not depend on the constant pressure condition. but I do
agree with Andreas Klamt when he says that we shall probably get to a point
in this discussion when it will become clear that we cannot compute
quantities
like translational entropies and/or free energies.

best regards,

Andre



&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&
Prof. Dr. André Farias de Moura
Departamento de Química
Universidade Federal de São Carlos
São Carlos - SP - Brasil
tel. 16-3351-8090
&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&


>
> Sent to CCL by: Andreas Klamt [klamt\a/cosmologic.de]
> Just a short reply:
> - I personly am not that happy that the cell method always is applied to
aqueous systems. Here we have strong contributions to enthalpy and
entropy for the formation of hydrogen bonds, ... Would your method also
apply for a cylohexane? If yes, what are the results?
> - I am confused by your statement that the solute reduces the entropy of
the solvent by the excluded volume: As far as I can see solvation is
usually considered at constant pressure, not at constant volume. It is
assumed that the solvent can get the missing volume elsewhere.
> - And I am not happy that you agree with my regarding the 3/2 vs. 5/2 RT
for the translational entropy of a molecule in the gasphase: Meanwhile
Frank Jensen told me that his erratum was wrong and that is should be
5/2, and he sent me a plausible derivation of that. The Atkins book also
says 5/2. When you look to the internet you find 3/2 and 5/2 about
equally often, and you find nice derivations for both. I am completely
confused now and have to clarify this for myself over Christmas. Is
there a difference in the ensembles considered? I do not find that in
the premisses of the literature derivations.
> - I admit that I did not take into account that in a classical ensemble
the reduction of the kinetic energy would correspond to a temperature
decrease. I myself am not sure about the degree of quantum effects here.
Anyway, in a quantum system we cannot do the integrals for position and
momentum separately and the discussion becomes useless.
>
> I am afraid that at the end of the discussion we will have to admit that
there is no way to define or to measure the translational entropy of a
solute in solution. I only can say that empirically we find the
> described significant free energy change of ~3 kcal/mol in the
> previously described A + A --> AA reaction, where all surface
> proportional, electrostatic, and hydrogen bonding interactions of AA are
just twice those of A.
>
> Best regards
>
> Andreas
>
>
>> Sent to CCL by: "Richard  Henchman" [henchman,manchester.ac.uk] It is
possible to regard a solute as having the ideal-gas entropy in
solution, but it is not the only possibility because there is no unique
way to allocate entropy to each molecule in the solution, as Raphael
Ribeiro (9 Dec) and Mike Gilson (11 Dec) have already pointed out.
>> This can be made clear by considering the example of water dissolved in
water (use D2O if you prefer to have labels and ignoring the fact that
it would form HOD). If you assign this solute water the ideal-gas
entropy (~129 J/K/mol at 298 K for water at the density of liquid
water), then the entropy of the surrounding water molecules is reduced
due to excluded volume by the solute, as is the common practice. This
ensures that the total entropy of the solution equals that of bulk
water. Another possibility is to give the solute water molecule the
same entropy of all the other water molecules i.e. less than the gas
phase (~70 J/K/mol at 298 K). How one could calculate such an entropy I
have shown in some recent publications on water:
>> http://link.aip.org/link/?JCP/126/064504 and a quantised version
http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/2008/112/i32/abs/jp0737303.html
These same ideas would apply to any solute, not just a solute water
molecule. The solute would have lower entropy than the ideas-gas value
due to confinement by the solvent. The solute takes all possible
positions and orientations but its freedom is still constrained by
where the other solvent molecules are. If this seems
>> counter-intuitive, it is only because the dimensionality of 3N-space is
so large. One could even consider a case intermediate between the
confined solute and the ideal-gas solute. In any case, whichever
solution model one uses, the solute and solvent entropy must add up to
give the total entropy of the solution. I think a number of
>> contributors to this discussion are right to question whether current
solvation models do this.
>> A few other comments: Andreas Klamt is correct to emphasise that the
ideal-gas entropy should be 3k/2 and not 5k/2 because the entropy
relates to a single molecule. However, I am not convinced by the
statement that "the solvent definitely reduces the motional (kinetic)
phase space". That amounts to saying that the solvent is at a lower
temperature. Ignoring quantum effects, which I believe to be small
(based on my second publication given above), the momentum partition
functions should be very similar.
>> Richard Henchman
>> __
>> Dr Richard H Henchman
>> The University of Manchester
>> http://personalpages.manchester.ac.uk/staff/henchman/
>
>
> --
> --------------------------------------------------------------------------
Dr. habil. Andreas Klamt
> COSMOlogic GmbH&CoKG
> Burscheider Str. 515
> 51381 Leverkusen, Germany
>
> Tel.: +49-2171-73168-1  Fax:  +49-2171-73168-9
> e-mail: klamt . cosmologic.de
> web:    www.cosmologic.de
> --------------------------------------------------------------------------
COSMOlogic
>        Your Competent Partner for
>        Computational Chemistry and Fluid Thermodynamics
> --------------------------------------------------------------------------
Please note our COSMO-RS Symposium in 2009
> (For details see: http://www.cosmologic.de/Symposium/symposium.html)>
>
>


From owner-chemistry@ccl.net Wed Dec 17 13:59:01 2008
From: "Ojwang, J.G.O. j.g.o.ojwang%a%tue.nl" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL: Lennard jones
Message-Id: <-38327-081217104712-8906-alPRVdsJtgTpXEhoLJQ+ng%x%server.ccl.net>
X-Original-From: "Ojwang, J.G.O." <j.g.o.ojwang%%tue.nl>
Content-Language: en-US
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Date: Wed, 17 Dec 2008 16:08:13 +0100
MIME-Version: 1.0


Sent to CCL by: "Ojwang, J.G.O." [j.g.o.ojwang- -tue.nl]
Have you checked on your timestep to ensure that there's no drift in energy=
?

Regards,
Ojwang' JGO
________________________________________
> From: owner-chemistry+j.g.o.ojwang=3D=3Dtue.nl|ccl.net [owner-chemistry+j.g=
.o.ojwang=3D=3Dtue.nl|ccl.net] On Behalf Of Leila Ramin lram5228**usyd.edu.=
au [owner-chemistry|ccl.net]
Sent: Wednesday, December 17, 2008 1:55 PM
To: Ojwang, J.G.O.
Subject: CCL: Lennard jones

Sent to CCL by: "Leila  Ramin" [lram5228__usyd.edu.au]
Hi,
I am doing MD for simple Lennard jones forces, I faced with the problem tha=
t when I apply Lennard jones, the atomes sometimes get too close to each ot=
her and the forces increase to infinity, How can I manage this problem.

Kind Regards
Leyla Ramin



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From owner-chemistry@ccl.net Wed Dec 17 18:43:00 2008
From: "Leyla Ramin l.ramin*aeromech.usyd.edu.au" <owner-chemistry[-]server.ccl.net>
To: CCL
Subject: CCL: Lennard jones
Message-Id: <-38328-081217183933-13755-Qy34UurLqywvJgettWgPGg[-]server.ccl.net>
X-Original-From: "Leyla Ramin" <l.ramin|-|aeromech.usyd.edu.au>
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Sent to CCL by: "Leyla Ramin" [l.ramin^-^aeromech.usyd.edu.au]
This is a multi-part message in MIME format.

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=20
Hi there,
=20
Thanks for your advise, Is there any available NVE ensemble code that I =
can use?
Kind Regards
Leyla Ramin

________________________________

> From: owner-chemistry+lram5228=3D=3Dusyd.edu.au**ccl.net on behalf of =
Ramon Crehuet rcsqtca/iqac.csic.es
Sent: Thu 18/12/2008 01:23
To: Leyla Ramin
Subject: CCL: Lennard jones




Sent to CCL by: Ramon Crehuet [rcsqtc^-^iqac.csic.es]
Hy Leila,
Reduce the time-step. Check for energy conservation and don't use
thermostats (use NVE ensemble) to check the parameters are stable.
Regards,

Ramon



Leila Ramin lram5228**usyd.edu.au wrote:
> Sent to CCL by: "Leila  Ramin" [lram5228__usyd.edu.au]
> Hi,
> I am doing MD for simple Lennard jones forces, I faced with the =
problem that when I apply Lennard jones, the atomes sometimes get too =
close to each other and the forces increase to infinity, How can I =
manage this problem.
>
> Kind Regards
> Leyla Ramin>
>
>



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<FONT face=3DTahoma size=3D2><B>From:</B> =
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<P><FONT size=3D2>Sent to CCL by: Ramon Crehuet =
[rcsqtc^-^iqac.csic.es]<BR>Hy Leila,<BR>Reduce the time-step. Check for =
energy conservation and don't use<BR>thermostats (use NVE ensemble) to =
check the parameters are =
stable.<BR>Regards,<BR><BR>Ramon<BR><BR><BR><BR>Leila Ramin =
lram5228**usyd.edu.au wrote:<BR>&gt; Sent to CCL by: "Leila&nbsp; Ramin" =
[lram5228__usyd.edu.au]<BR>&gt; Hi,<BR>&gt; I am doing MD for simple =
Lennard jones forces, I faced with the problem that when I apply Lennard =
jones, the atomes sometimes get too close to each other and the forces =
increase to infinity, How can I manage this problem.<BR>&gt;<BR>&gt; =
Kind Regards<BR>&gt; Leyla Ramin&gt;<BR>&gt;<BR>&gt;<BR><BR><BR><BR>-=3D =
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