Re: [gmx-users] issue in replica exchange
Yes, my system is described at atomic level. No, I can't see any "strange" value around exchanges. I analyzed only a very little number of trajectories, but temperature, volume, potential energy, pressure seem all to be around normal fluctuations. 2013/5/2 XAvier Periole > > Did you look at some data like temperature/pressure/box size/Epot as a > function of time and especially around some exchanges? > > Your system is atomistic I presume. > > On May 2, 2013, at 12:38 PM, Simone Conti wrote: > > > I'm running remd in NPT ensemble for a small peptide and all is ok if the > > maximum temperature is below 510/520 kelvin. I use Nosé-Hoover termostat > > and Parrinello-Rahman barostat. Ref T from 285 to 500K and ref P equals > to > > 1bar. Gromacs version 4.5.5. Exchange trials every 5 ps. > > If I try to add replica at a higher temperature the system crash, but I > > think it is a problem of equilibration. > > > > > > 2013/5/1 XAvier Periole > > > >> > >> Ok here is my current status on that REMD issue. > >> > >> For info: I use > >> Temperature: v-rescale, tau_t = 2.0 ps > >> Pressure: berendsen, tau_p = 5.0 ps, > >> time step: dt=0.002 - 0.020 fs, > >> COM removal on for bilayer/water separately > >> > >> The symptoms: explosion of the system after 2-5 steps following the > swap, > >> first sign is a huge jump in LJ interactions and pressure. This jump > seems > >> to be absorbed by the box size and temperature when possible … see > example > >> I provided earlier. A large VCM (velocity centre of mass?) is often > >> associated with the crash. But also pressure scaling more than 1% ... > >> > >> 1- the problem mentioned above remains in gmx-4.5.7 and it might > actually > >> got worse. I was able to run a 500 ns simulation with gmx405 using > similar > >> setup as for gmx457. The following point happened in gmx457. > >> 2- it persists with a time step of 2 fs. Actually all tests performed in > >> the following used dt=2fs. > >> 3- if I perform an exchange that explodes within mdrun myself > (externally > >> to the remd gromacs by getting the gro file with the mdp adjusting the > >> temperature) it goes all fine. > >> 4- the issue gets much worst when the consecutive replicas differ > >> (different protein conformations and the box size etc) … explosion at > first > >> exchange. > >> 5- the use of parrinelo-raman does not help > >> 6- cancelling the centre of mass removal does not remove the problem. > >> 7- switching to NVT ensemble does not help but makes it worst (crash in > 2 > >> steps). All exchanges accepted at first attempt crash with the message > >> "Large VCM(group SOL): -0.0XXX , -0.XXX, -0.16XXX, Temp-cm:6.55XXX > >> 8- using a unique conformation (the same) for all replicas in the NVT > REMD > >> simulation after equilibration in the same NVT ensemble (for 1 ns) > removes > >> the problem. > >> 9- taking the equilibrated NVT conformations, equilibrate them in an NPT > >> ensemble (1 ns) and let go the exchanges afterwards restores the > problem … > >> one exchange is not properly done at the second trial, while the first > ones > >> were fine. Well if errors were made that was with reasonable > >> 10- note also that the coarse grain I use is extremely forgiving, > meaning > >> you can perform really nasty transformations and run it further after > >> simple minimisation … so even abrupt changes in temperatures should be > fine > >> and relax quickly. > >> 11- when looking at the conformations themselves nothing appears to have > >> jumped over or nothing funky. > >> > >> At this point I am not sure what to think and what to do next. There is > >> definitely something not going right during the exchanges. > >> > >> Anyone has been able to run a REMD simulation in an NPT ensemble without > >> crashes? I would imagine someone has and something particular to my > system > >> is making it going wrong but I am really wondering what it could be. My > >> feeling is that something relative to the box size or pressure is not > going > >> across but it might be something completely different, when the > consecutive > >> systems differ reasonably. > >> > >> However that would suggest that the manner the exchanges are made is > >> severely wrong in some cases. > >> > >> Any help to resolve the problem would be g
Re: [gmx-users] issue in replica exchange
I'm running remd in NPT ensemble for a small peptide and all is ok if the
maximum temperature is below 510/520 kelvin. I use Nosé-Hoover termostat
and Parrinello-Rahman barostat. Ref T from 285 to 500K and ref P equals to
1bar. Gromacs version 4.5.5. Exchange trials every 5 ps.
If I try to add replica at a higher temperature the system crash, but I
think it is a problem of equilibration.
2013/5/1 XAvier Periole
>
> Ok here is my current status on that REMD issue.
>
> For info: I use
> Temperature: v-rescale, tau_t = 2.0 ps
> Pressure: berendsen, tau_p = 5.0 ps,
> time step: dt=0.002 - 0.020 fs,
> COM removal on for bilayer/water separately
>
> The symptoms: explosion of the system after 2-5 steps following the swap,
> first sign is a huge jump in LJ interactions and pressure. This jump seems
> to be absorbed by the box size and temperature when possible … see example
> I provided earlier. A large VCM (velocity centre of mass?) is often
> associated with the crash. But also pressure scaling more than 1% ...
>
> 1- the problem mentioned above remains in gmx-4.5.7 and it might actually
> got worse. I was able to run a 500 ns simulation with gmx405 using similar
> setup as for gmx457. The following point happened in gmx457.
> 2- it persists with a time step of 2 fs. Actually all tests performed in
> the following used dt=2fs.
> 3- if I perform an exchange that explodes within mdrun myself (externally
> to the remd gromacs by getting the gro file with the mdp adjusting the
> temperature) it goes all fine.
> 4- the issue gets much worst when the consecutive replicas differ
> (different protein conformations and the box size etc) … explosion at first
> exchange.
> 5- the use of parrinelo-raman does not help
> 6- cancelling the centre of mass removal does not remove the problem.
> 7- switching to NVT ensemble does not help but makes it worst (crash in 2
> steps). All exchanges accepted at first attempt crash with the message
> "Large VCM(group SOL): -0.0XXX , -0.XXX, -0.16XXX, Temp-cm:6.55XXX
> 8- using a unique conformation (the same) for all replicas in the NVT REMD
> simulation after equilibration in the same NVT ensemble (for 1 ns) removes
> the problem.
> 9- taking the equilibrated NVT conformations, equilibrate them in an NPT
> ensemble (1 ns) and let go the exchanges afterwards restores the problem …
> one exchange is not properly done at the second trial, while the first ones
> were fine. Well if errors were made that was with reasonable
> 10- note also that the coarse grain I use is extremely forgiving, meaning
> you can perform really nasty transformations and run it further after
> simple minimisation … so even abrupt changes in temperatures should be fine
> and relax quickly.
> 11- when looking at the conformations themselves nothing appears to have
> jumped over or nothing funky.
>
> At this point I am not sure what to think and what to do next. There is
> definitely something not going right during the exchanges.
>
> Anyone has been able to run a REMD simulation in an NPT ensemble without
> crashes? I would imagine someone has and something particular to my system
> is making it going wrong but I am really wondering what it could be. My
> feeling is that something relative to the box size or pressure is not going
> across but it might be something completely different, when the consecutive
> systems differ reasonably.
>
> However that would suggest that the manner the exchanges are made is
> severely wrong in some cases.
>
> Any help to resolve the problem would be greatly appreciated.
>
> XAvier.
>
> On Apr 26, 2013, at 9:21 AM, Mark Abraham
> wrote:
>
> > On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole
> wrote:
> >
> >>
> >> Thanks for the answer. I'll check gmx4.5.7 and report back.
> >>
> >> I am not sure what you mean by GROMACS swaps the coordinates not the
> >> ensemble data. The coupling to P and T and not exchanged with it?
> >
> >
> > The code in src/kernel/repl_ex.c:
> >
> > static void exchange_state(const gmx_multisim_t *ms, int b, t_state
> *state)
> > {
> >/* When t_state changes, this code should be updated. */
> >int ngtc, nnhpres;
> >ngtc= state->ngtc * state->nhchainlength;
> >nnhpres = state->nnhpres* state->nhchainlength;
> >exchange_rvecs(ms, b, state->box, DIM);
> >exchange_rvecs(ms, b, state->box_rel, DIM);
> >exchange_rvecs(ms, b, state->boxv, DIM);
> >exchange_reals(ms, b, &(state->veta), 1);
> >exchange_reals(ms, b, &(state->vol0), 1);
> >exchange_rvecs(ms, b, state->svir_prev, DIM);
> >exchange_rvecs(ms, b, state->fvir_prev, DIM);
> >exchange_rvecs(ms, b, state->pres_prev, DIM);
> >exchange_doubles(ms, b, state->nosehoover_xi, ngtc);
> >exchange_doubles(ms, b, state->nosehoover_vxi, ngtc);
> >exchange_doubles(ms, b, state->nhpres_xi, nnhpres);
> >exchange_doubles(ms, b, state->nhpres_vxi, nnhpres);
> >exchange_doubles(ms, b, state->therm_integral, state->ngtc);
> >exchange_rvecs(ms, b, state
Re: [gmx-users] doubt in remd
Hi! I'm also working on REMD in these days. For temperature spacing you can use this web site: http://folding.bmc.uu.se/remd/ In order to find the most probable structure, which should be the global minimum, I think you can work with cluster analysis based on rmsd. Or it can be also useful a secondary structure analysis along the trajectory (if it is interesting for your system). If anyone else have some ideas I'm also looking for them. Simone 2013/4/9 Nikunj Maheshwari > Hi. Glad to know that your REMD was successful. We are trying to do the > same, but are stuck in between. > Can you tell us, how did you got the temperature spacing? > Thanks > > On Tue, Apr 9, 2013 at 11:59 AM, Shine A wrote: > > > Respected sir, > > > > I successfully completed REMD simulation. Now I am > > struggling with analysis part. Here how I select the global minimum from > > replica? Can you give some suggestions about the analysis part? > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
