[gmx-users] v-rescale - harmonic oscillator

Berk Hess gmx3 at hotmail.com
Thu May 7 14:27:20 CEST 2009 

Hi,

With a diatomic molecule there is the issue that the rotation of the molecule has two degrees of freedom
which are completely uncoupled from the rest of the system.

Anyhow, I made a 1D harmonic oscillator using a position restraint and even there the energy
does not seem to be conserved.
I am not sure if a harmonic oscillator is a pathetic case, like with Nose-Hoover,
or if this is an issue with the integrator implementation in Gromacs.
I might need to ask Bussi about this.

Berk

> From: servaas.michielssens at student.kuleuven.be
> To: gmx-users at gromacs.org
> Date: Thu, 7 May 2009 14:03:30 +0200
> Subject: [gmx-users] v-rescale - harmonic oscillator
> 
> Hi,
> 
> It is just a diatomic molecule without other interactions (so only
> bonded interaction, LJ=0 and charges=0 on the atoms). What other details
> would you like to know? Should I send you the tpr file?
> 
> Servaas
> 
> 
> 
> > 
> > 
> > Hi,
> > 
> > No, only for small values is should be off, maybe tau_t < 10 or 100 * delta_t.
> > 
> > How did you set up your harmonic oscillator?
> > 
> > Berk
> > 
> > > From: servaas.michielssens at student.kuleuven.be
> > > To: gmx-users at gromacs.org
> > > Date: Thu, 7 May 2009 12:54:54 +0200
> > > Subject: [gmx-users] Re:  v-rescale - harmonic oscillator
> > > 
> > > Hi,
> > > 
> > > Thank you for your reply.
> > > 
> > > Yes by effective energy I mean the Gromacs conserved energy term.
> > > 
> > > So you would say the cause of my problem here is that I need a small
> > > tau_t to thermostat this system but for small tau_t values the algorithm
> > > is not 100% ok yet? And what are very small tau_t values? I tested with
> > > quite a big range here.
> > > 
> > > The problem occurred to me when I was experimenting with a hybrid monte
> > > carlo algorithm. I first tested it on a noble gas and compared to MD
> > > simulation with nose-hoover and v-rescale. Those results were 100%
> > > identical. Then I tried it on a dipeptide in vacuum, results were a
> > > little off here (I would expect this for nose-hoover thermostat, but not
> > > for v-rescale). So I decided to go the the extreme simple case of a
> > > harmonic oscillator. Those results were seriously off, and then I
> > > checked the conserved energy term, which seems impossible to keep it
> > > conserved for this system. (of course there can also be an error in my
> > > hybrid monte carlo code, but the fact that the conserved energy is not
> > > conserved is disturbing me here)
> > > 
> > > 
> > > Servaas
> > > 
> > > 
> > > 
> > > 
> > > Hi,
> > > 
> > > What do you mean with effective energy?
> > > The Gromacs conserved energy term?
> > > 
> > > For very small tau_t the current implementation does not work well.
> > > Bussi mailed me a proper implementation that I will put in when I have time.
> > > 
> > > Berk
> > > 
> > > > From: servaas.michielssens at student.kuleuven.be
> > > > To: gmx-users at gromacs.org
> > > > Date: Thu, 7 May 2009 09:02:52 +0200
> > > > Subject: [gmx-users] v-rescale - harmonic oscillator
> > > > 
> > > > Hi,
> > > > 
> > > > I did some experiments with a harmonic oscillator (diatomic molecule
> > > > without charge en LJ parameters) using the v-rescale thermostat. First I
> > > > ran a simulation in the NVE ensemble with a time-step of 0.0001ps, total
> > > > energy was constant here. 
> > > > 
> > > > Then I tried simulating the system with the v-rescale thermostat, same
> > > > time-step of 0.0001ps and tau_t=100,10,1,0.1,0.01,0.001. For none of
> > > > those simulations the effective energy was conserved. 
> > > > (effective energy should be a conserved quantity for NVT simulations
> > > > with v-rescale thermostat, JOURNAL OF CHEMICAL PHYSICS    Volume: 126
> > > > Issue: 1  Article Number: 014101    Published: JAN 7 2007 )
> > > > 
> > > > So what is going wrong here? Would one expect this thermostat to fail
> > > > for such system (e.g. a simple Nose-Hoover is known to fail for the
> > > > harmonic oscillator)? 
> > > > 
> > > > 
> > > > Thanks in advance,
> > > > 
> > > > Servaas
> > > > 
> > > 
> > > _______________________________________________
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> > ------------------------------
> > 
> > Message: 5
> > Date: Thu, 07 May 2009 12:29:31 +0100
> > From: TJ Piggot <t.piggot at bristol.ac.uk>
> > Subject: Re: [gmx-users] atom name O3PB not found in residue ATP 340
> > 	while	generating exclusions when running pdb2gmx
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <287C7FBF56A3D6F2F0A5C65F at localhost.localdomain>
> > Content-Type: text/plain; charset=us-ascii; format=flowed
> > 
> > I agree with Justin that the way to do this is by adding a new entry to the 
> > .rtp file. The only point I would make is that as you seem to be missing 
> > the gamma phosphate and its oxygens would it not make more sense to start 
> > from an ADP topology? Also you should ask (or have asked) yourself why 
> > these atoms are missing in your start structure and do they need to be 
> > added back or are they missing for a purpose.
> > 
> > Tom
> > 
> > --On Thursday, May 07, 2009 06:59:21 -0400 "Justin A. Lemkul" 
> > <jalemkul at vt.edu> wrote:
> > 
> > >
> > >
> > > Una Bjarnadottir wrote:
> > >> Dear all,
> > >>
> > >> I'm running a simulation of a structure which has part of ATP bound to
> > >> it so I'm using the -missing command when running pdb2gmx
> > >>
> > >> pdb2gmx runs and lists the missing atoms and than it gives a fatal error
> > >> about missing atom name!
> > >>
> > >> WARNING: atom O3PB is missing in residue ATP 340 in the pdb file
> > >> WARNING: atom APG is missing in residue ATP 340 in the pdb file
> > >> WARNING: atom O1PG is missing in residue ATP 340 in the pdb file
> > >> WARNING: atom O2PG is missing in residue ATP 340 in the pdb file
> > >> WARNING: atom O3PG is missing in residue ATP 340 in the pdb file
> > >> WARNING: atom H3PG is missing in residue ATP 340 in the pdb file
> > >>         You might need to add atom H3PG to the hydrogen database of
> > >> residue ATP
> > >>         in the file ff???.hdb (see the manual)
> > >>
> > >> There were 17 missing atoms in molecule Protein_A
> > >> Number of bonds was 3730, now 3725
> > >> Generating angles, dihedrals and pairs...
> > >> Fatal error: atom name O3PB not found in residue ATP 340 while
> > >> generating exclusions
> > >>
> > >
> > > The [ exclusions ] are pre-defined in the force field .rtp file.  The
> > > easiest way I can see to get around this is to make a local copy of the
> > > .rtp file, make a new entry for your molecule based on the ATP entry
> > > (deleting out whatever atoms are not present) and trying again, using a
> > > new name for this partial ATP, in both the .rtp and .pdb files.
> > >
> > > The -missing option, as described by pdb2gmx is "dangerous" for this
> > > reason.
> > >
> > > -Justin
> > >> How can I resolve this  first not done by -missing command?
> > >>
> > >> Cheers, Una
> > >>
> > >
> > > --
> > > ========================================
> > >
> > > Justin A. Lemkul
> > > Ph.D. Candidate
> > > ICTAS Doctoral Scholar
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > > ========================================
> > > _______________________________________________
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> > 
> > 
> > 
> > ----------------------
> > TJ Piggot
> > t.piggot at bristol.ac.uk
> > University of Bristol, UK.
> > 
> > 
> > 
> > ------------------------------
> > 
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> > End of gmx-users Digest, Vol 61, Issue 22
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