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: [email protected] > > To: [email protected] > > 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 > > > > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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]. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _________________________________________________________________ > Express yourself instantly with MSN Messenger! Download today it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090507/2f780925/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Thu, 07 May 2009 12:29:31 +0100 > From: TJ Piggot <[email protected]> > 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 <[email protected]> > Message-ID: <[email protected]> > 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" > <[email protected]> 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 > > > > ======================================== > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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]. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ---------------------- > TJ Piggot > [email protected] > University of Bristol, UK. > > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 61, Issue 22 > ***************************************** > _______________________________________________ gmx-users mailing list [email protected] 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]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
