[gmx-users] RE: RE : FEP : separating components of dgdl
Berk Hess
gmx3 at hotmail.com
Tue Jan 29 15:08:31 CET 2008
I overlooked that you printed dVdl, not dGdl.
Without looking into the code, I would not know where term is missing.
Can you figure out if any energy terms are missing in the print?
Please check if all energy terms in de log file are present in the dvdl print.
I would guess that the dvdl numbers are correct, but there could be a mistake
in there as well.
Selectively turning off perturbations would find it, but that is a bit of work.
Berk.
> It is a single processor simulation.
>
> As I change some masses,I have indeed a change in Ekin (-1,23e+00) , but it should not explain what happens with Vpot, should it ?
> I also have position restraints whose parameters do not change, so dVdl should be 0, which is what it reads. I did
> not copy this in my previous mail, I should have.
>
> Thanks for your help,
> Michael Bon
>
>
> -------- Message d'origine--------
> De: gmx-users-bounces at gromacs.org de la part de gmx-users-request at gromacs.org
> Date: mar. 29/01/2008 12:00
> À: gmx-users at gromacs.org
> Objet : gmx-users Digest, Vol 45, Issue 116
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> Today's Topics:
>
> 1. Re: dihedral restraints wiki section (Behnoush Zare)
> 2. RE : FEP : separating components of dgdl (BON Michael)
> 3. RE: RE : FEP : separating components of dgdl (Berk Hess)
> 4. Re: dihedral restraints wiki section (Xavier Periole)
> 5. Re: GROMACS ON CYGWIN. (Nabajyoti Goswami)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 29 Jan 2008 13:06:14 +0330 (IRST)
> From: Behnoush Zare <bzare at iums.ac.ir>
> Subject: Re: [gmx-users] dihedral restraints wiki section
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <26532812.27691201599374219.JavaMail.root at zimbra.iums.ac.ir>
> Content-Type: text/plain; charset=utf-8
>
> Dear chris,
>
> Thank you for your help about performing dihedral restraints. Would you please kindly explain to me how I can measure the value of dihedral angles between two amin acids (I mean C'-N-C-C' and N-C-C'-N).
> Thank you in advance for your valuable aid.
>
> Behnoush
>
> ----- Original Message -----
> From: "chris neale" <chris.neale at utoronto.ca>
> To: gmx-users at gromacs.org
> Sent: Sunday, January 27, 2008 11:49:42 PM (GMT+0330) Asia/Tehran
> Subject: [gmx-users] dihedral restraints wiki section
>
> I have added a section on dihedral restraints to the wiki.
>
> http://wiki.gromacs.org/index.php/Dihedral_Restraints
>
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> ------------------------------
>
> Message: 2
> Date: Tue, 29 Jan 2008 10:24:57 +0100
> From: "BON Michael" <michael.bon at cea.fr>
> Subject: [gmx-users] RE : FEP : separating components of dgdl
> To: <gmx-users at gromacs.org>
> Message-ID:
> <92F41516EE90B540BC03B8C4613EF6B933CC72 at DIODON.extra.cea.fr>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Thanks for the quick reply.
>
> I have an other question : I ran a quick simulation on a single node using mdrun -sepdvdl and the components are written in
> the .log file. But the final value of dVpot/dlambda doesn't seem to be the sum of the components above. Example for some step:
>
> VdW and Coulomb SR : dVdl -2.72859e+02
> Angle : dVdl 3.56537e+00
> Proper Dih. : dVdl -7.31260e-03
> Ryckaert-Bell. : dVdl -1.13654e-01
> LJ-14 + Coulomb-14 : dVdl 6.39499e+02
> Dispersion correc. : dVdl 0.00000e+00
>
> And I read : dVpot/dlambda = 3.62310e+02, instead of 3.70e+02.
>
> There is no PME in this sim.
>
> What did I forget ?
>
> Many thanks in advance,
>
> Michaël Bon
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> ------------------------------
>
> Message: 3
> Date: Tue, 29 Jan 2008 10:32:08 +0100
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: [gmx-users] RE: RE : FEP : separating components of dgdl
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BLU134-W229F0850B9736B358C55858E350 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
>
> ----------------------------------------
> > Date: Tue, 29 Jan 2008 10:24:57 +0100
> > From: michael.bon at cea.fr
> > To: gmx-users at gromacs.org
> > Subject: RE : FEP : separating components of dgdl
> >
> >
> > Thanks for the quick reply.
> >
> > I have an other question : I ran a quick simulation on a single node using mdrun -sepdvdl and the components are written in
> > the .log file. But the final value of dVpot/dlambda doesn't seem to be the sum of the components above. Example for some step:
> >
> > VdW and Coulomb SR : dVdl -2.72859e+02
> > Angle : dVdl 3.56537e+00
> > Proper Dih. : dVdl -7.31260e-03
> > Ryckaert-Bell. : dVdl -1.13654e-01
> > LJ-14 + Coulomb-14 : dVdl 6.39499e+02
> > Dispersion correc. : dVdl 0.00000e+00
> >
> > And I read : dVpot/dlambda = 3.62310e+02, instead of 3.70e+02.
> >
> > There is no PME in this sim.
> >
> > What did I forget ?
>
> I assume you are running single processor.
> The terms are per processor.
>
> I think that the only contributions that are no added are:
> constraints, only when you change constraint lengths,
> kinetic energy, only when you change masses.
>
> So do you change constraint lengths or masses?
>
> Berk.
>
> _________________________________________________________________
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> ------------------------------
>
> Message: 4
> Date: Tue, 29 Jan 2008 10:47:45 +0100
> From: "Xavier Periole" <X.Periole at rug.nl>
> Subject: Re: [gmx-users] dihedral restraints wiki section
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <web-65336809 at mail3.rug.nl>
> Content-Type: text/plain;charset=utf-8;format="flowed"
>
>
>
> > Thank you for your help about performing dihedral restraints. Would you
> >please kindly explain to me how I can measure the value of dihedral angles
> >between two amin acids (I mean C'-N-C-C' and N-C-C'-N).
> > Thank you in advance for your valuable aid.
>
> Well this should really be easy to find out! check out the manual,
> there is section ANALYSIS ... g_angle is one option.
>
> >
> > Behnoush
> >
> > ----- Original Message -----
> >From: "chris neale" <chris.neale at utoronto.ca>
> > To: gmx-users at gromacs.org
> > Sent: Sunday, January 27, 2008 11:49:42 PM (GMT+0330) Asia/Tehran
> > Subject: [gmx-users] dihedral restraints wiki section
> >
> > I have added a section on dihedral restraints to the wiki.
> >
> > http://wiki.gromacs.org/index.php/Dihedral_Restraints
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
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> -----------------------------------------------------
> XAvier Periole - PhD
>
> NMR & Molecular Dynamics Group
> University of Groningen
> The Netherlands
> http://md.chem.rug.nl/~periole
> -----------------------------------------------------
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 29 Jan 2008 15:21:37 +0530
> From: "Nabajyoti Goswami" <nabajyoti.goswami at gmail.com>
> Subject: Re: [gmx-users] GROMACS ON CYGWIN.
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <e14f21f70801290151y7f59cd6fq9539d1a509836e68 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> If you are in windows and want to use gromacs by cygwin I suggest you to use
> the window version of gromacs. place all gromacs executable into
> C:/cygwin/home/bin *or* C:/windows/system32. It must work.
>
> On Jan 28, 2008 8:29 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
> > DAVID RINCON wrote:
> > > Good morning people,
> > >
> > > I want to install gromacs on my laptop and I have installed cygwin and
> > > some necessery gromacs libraries as fftw. But, when I am going to
> > install,
> > >
> > > glibc
> > >
> > > just in the first step with ./configure. That broke down. :S
> >
> > Imagine I rang my car mechanic and told him that the car was borken and
> > the spare tyre was making a weird noise, and asked him what was wrong...
> > He'd ask me to bring him the car or describe the problem better. :-)
> >
> > > Someone has installed gromacs on their computers?
> > > How can I do it?
> >
> > Start here http://wiki.gromacs.org/index.php/GROMACS_on_Windows and
> > check out the general advice here
> > http://www.catb.org/~esr/faqs/smart-questions.html<http://www.catb.org/%7Eesr/faqs/smart-questions.html>
> >
> > Mark
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> Regads,
> Nabajyoti Goswami
>
>
>
>
>
>
>
>
>
>
>
>
> Ph.D Student.
> Center for Biotechnology,
> Anna University,
> Chennai-600025
> Tamil Nadu.
> Mobile: 09840487093
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