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--------
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Date: mar. 29/01/2008 12:00
À: gmx-users@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 <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] dihedral restraints wiki section
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]>
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" <[EMAIL PROTECTED]>
To: gmx-users@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" <[EMAIL PROTECTED]>
Subject: [gmx-users] RE : FEP : separating components of dgdl
To: <gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]>
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 <[EMAIL PROTECTED]>
Subject: [gmx-users] RE: RE : FEP : separating components of dgdl
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
----------------------------------------
> Date: Tue, 29 Jan 2008 10:24:57 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@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" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] dihedral restraints wiki section
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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" <[EMAIL PROTECTED]>
> To: gmx-users@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@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 [EMAIL PROTECTED]
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>
> _______________________________________________
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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" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] GROMACS ON CYGWIN.
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]>
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 <[EMAIL PROTECTED]> 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@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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> www interface or send it to [EMAIL PROTECTED]
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>
Regads,
Nabajyoti Goswami
Ph.D Student.
Center for Biotechnology,
Anna University,
Chennai-600025
Tamil Nadu.
Mobile: 09840487093
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