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Hi,<br><br>With a diatomic molecule there is the issue that the rotation of the molecule has two degrees of freedom<br>which are completely uncoupled from the rest of the system.<br><br>Anyhow, I made a 1D harmonic oscillator using a position restraint and even there the energy<br>does not seem to be conserved.<br>I am not sure if a harmonic oscillator is a pathetic case, like with Nose-Hoover,<br>or if this is an issue with the integrator implementation in Gromacs.<br>I might need to ask Bussi about this.<br><br>Berk<br><br>> From: servaas.michielssens@student.kuleuven.be<br>> To: gmx-users@gromacs.org<br>> Date: Thu, 7 May 2009 14:03:30 +0200<br>> Subject: [gmx-users] v-rescale - harmonic oscillator<br>> <br>> Hi,<br>> <br>> It is just a diatomic molecule without other interactions (so only<br>> bonded interaction, LJ=0 and charges=0 on the atoms). What other details<br>> would you like to know? Should I send you the tpr file?<br>> <br>> Servaas<br>> <br>> <br>> <br>> > <br>> > <br>> > Hi,<br>> > <br>> > No, only for small values is should be off, maybe tau_t < 10 or 100 * delta_t.<br>> > <br>> > How did you set up your harmonic oscillator?<br>> > <br>> > Berk<br>> > <br>> > > From: servaas.michielssens@student.kuleuven.be<br>> > > To: gmx-users@gromacs.org<br>> > > Date: Thu, 7 May 2009 12:54:54 +0200<br>> > > Subject: [gmx-users] Re: v-rescale - harmonic oscillator<br>> > > <br>> > > Hi,<br>> > > <br>> > > Thank you for your reply.<br>> > > <br>> > > Yes by effective energy I mean the Gromacs conserved energy term.<br>> > > <br>> > > So you would say the cause of my problem here is that I need a small<br>> > > tau_t to thermostat this system but for small tau_t values the algorithm<br>> > > is not 100% ok yet? And what are very small tau_t values? I tested with<br>> > > quite a big range here.<br>> > > <br>> > > The problem occurred to me when I was experimenting with a hybrid monte<br>> > > carlo algorithm. I first tested it on a noble gas and compared to MD<br>> > > simulation with nose-hoover and v-rescale. Those results were 100%<br>> > > identical. Then I tried it on a dipeptide in vacuum, results were a<br>> > > little off here (I would expect this for nose-hoover thermostat, but not<br>> > > for v-rescale). So I decided to go the the extreme simple case of a<br>> > > harmonic oscillator. Those results were seriously off, and then I<br>> > > checked the conserved energy term, which seems impossible to keep it<br>> > > conserved for this system. (of course there can also be an error in my<br>> > > hybrid monte carlo code, but the fact that the conserved energy is not<br>> > > conserved is disturbing me here)<br>> > > <br>> > > <br>> > > Servaas<br>> > > <br>> > > <br>> > > <br>> > > <br>> > > Hi,<br>> > > <br>> > > What do you mean with effective energy?<br>> > > The Gromacs conserved energy term?<br>> > > <br>> > > For very small tau_t the current implementation does not work well.<br>> > > Bussi mailed me a proper implementation that I will put in when I have time.<br>> > > <br>> > > Berk<br>> > > <br>> > > > From: servaas.michielssens at student.kuleuven.be<br>> > > > To: gmx-users at gromacs.org<br>> > > > Date: Thu, 7 May 2009 09:02:52 +0200<br>> > > > Subject: [gmx-users] v-rescale - harmonic oscillator<br>> > > > <br>> > > > Hi,<br>> > > > <br>> > > > I did some experiments with a harmonic oscillator (diatomic molecule<br>> > > > without charge en LJ parameters) using the v-rescale thermostat. First I<br>> > > > ran a simulation in the NVE ensemble with a time-step of 0.0001ps, total<br>> > > > energy was constant here. <br>> > > > <br>> > > > Then I tried simulating the system with the v-rescale thermostat, same<br>> > > > time-step of 0.0001ps and tau_t=100,10,1,0.1,0.01,0.001. For none of<br>> > > > those simulations the effective energy was conserved. <br>> > > > (effective energy should be a conserved quantity for NVT simulations<br>> > > > with v-rescale thermostat, JOURNAL OF CHEMICAL PHYSICS Volume: 126<br>> > > > Issue: 1 Article Number: 014101 Published: JAN 7 2007 )<br>> > > > <br>> > > > So what is going wrong here? Would one expect this thermostat to fail<br>> > > > for such system (e.g. a simple Nose-Hoover is known to fail for the<br>> > > > harmonic oscillator)? <br>> > > > <br>> > > > <br>> > > > Thanks in advance,<br>> > > > <br>> > > > Servaas<br>> > > > <br>> > > <br>> > > _______________________________________________<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the <br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> > _________________________________________________________________<br>> > Express yourself instantly with MSN Messenger! Download today it's FREE!<br>> > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/<br>> > -------------- next part --------------<br>> > An HTML attachment was scrubbed...<br>> > URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090507/2f780925/attachment-0001.html<br>> > <br>> > ------------------------------<br>> > <br>> > Message: 5<br>> > Date: Thu, 07 May 2009 12:29:31 +0100<br>> > From: TJ Piggot <t.piggot@bristol.ac.uk><br>> > Subject: Re: [gmx-users] atom name O3PB not found in residue ATP 340<br>> >         while        generating exclusions when running pdb2gmx<br>> > To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> > Message-ID: <287C7FBF56A3D6F2F0A5C65F@localhost.localdomain><br>> > Content-Type: text/plain; charset=us-ascii; format=flowed<br>> > <br>> > I agree with Justin that the way to do this is by adding a new entry to the <br>> > .rtp file. The only point I would make is that as you seem to be missing <br>> > the gamma phosphate and its oxygens would it not make more sense to start <br>> > from an ADP topology? Also you should ask (or have asked) yourself why <br>> > these atoms are missing in your start structure and do they need to be <br>> > added back or are they missing for a purpose.<br>> > <br>> > Tom<br>> > <br>> > --On Thursday, May 07, 2009 06:59:21 -0400 "Justin A. Lemkul" <br>> > <jalemkul@vt.edu> wrote:<br>> > <br>> > ><br>> > ><br>> > > Una Bjarnadottir wrote:<br>> > >> Dear all,<br>> > >><br>> > >> I'm running a simulation of a structure which has part of ATP bound to<br>> > >> it so I'm using the -missing command when running pdb2gmx<br>> > >><br>> > >> pdb2gmx runs and lists the missing atoms and than it gives a fatal error<br>> > >> about missing atom name!<br>> > >><br>> > >> WARNING: atom O3PB is missing in residue ATP 340 in the pdb file<br>> > >> WARNING: atom APG is missing in residue ATP 340 in the pdb file<br>> > >> WARNING: atom O1PG is missing in residue ATP 340 in the pdb file<br>> > >> WARNING: atom O2PG is missing in residue ATP 340 in the pdb file<br>> > >> WARNING: atom O3PG is missing in residue ATP 340 in the pdb file<br>> > >> WARNING: atom H3PG is missing in residue ATP 340 in the pdb file<br>> > >> You might need to add atom H3PG to the hydrogen database of<br>> > >> residue ATP<br>> > >> in the file ff???.hdb (see the manual)<br>> > >><br>> > >> There were 17 missing atoms in molecule Protein_A<br>> > >> Number of bonds was 3730, now 3725<br>> > >> Generating angles, dihedrals and pairs...<br>> > >> Fatal error: atom name O3PB not found in residue ATP 340 while<br>> > >> generating exclusions<br>> > >><br>> > ><br>> > > The [ exclusions ] are pre-defined in the force field .rtp file. The<br>> > > easiest way I can see to get around this is to make a local copy of the<br>> > > .rtp file, make a new entry for your molecule based on the ATP entry<br>> > > (deleting out whatever atoms are not present) and trying again, using a<br>> > > new name for this partial ATP, in both the .rtp and .pdb files.<br>> > ><br>> > > The -missing option, as described by pdb2gmx is "dangerous" for this<br>> > > reason.<br>> > ><br>> > > -Justin<br>> > >> How can I resolve this first not done by -missing command?<br>> > >><br>> > >> Cheers, Una<br>> > >><br>> > ><br>> > > --<br>> > > ========================================<br>> > ><br>> > > Justin A. Lemkul<br>> > > Ph.D. Candidate<br>> > > ICTAS Doctoral Scholar<br>> > > Department of Biochemistry<br>> > > Virginia Tech<br>> > > Blacksburg, VA<br>> > > jalemkul[at]vt.edu | (540) 231-9080<br>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> > ><br>> > > ========================================<br>> > > _______________________________________________<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the www<br>> > > interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> > <br>> > <br>> > ----------------------<br>> > TJ Piggot<br>> > t.piggot@bristol.ac.uk<br>> > University of Bristol, UK.<br>> > <br>> > <br>> > <br>> > ------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list<br>> > gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > <br>> > End of gmx-users Digest, Vol 61, Issue 22<br>> > *****************************************<br>> > <br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. 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