I mean tpr files not tar! Autocorrection is sometimes funny :))
On May 2, 2013, at 2:11 PM, XAvier Periole <x.peri...@rug.nl> wrote:
>
> Could you send me a set of tar files that I could look at things the same way
> I do with my system? I would guess that 6 tar files where you same energies
> and print log file every step but xtc and trr files not that often would be
> really cool.
>
> You can send them directly to my email (x.peri...@rug.nl) unless they are too
> big. If you do not like the idea it is also ok.
>
> On May 2, 2013, at 1:38 PM, Simone Conti <simone...@gmail.com> wrote:
>
>> 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 <x.peri...@rug.nl>
>>
>>>
>>> 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 <simone...@gmail.com> 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 <x.peri...@rug.nl>
>>>>
>>>>>
>>>>> 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 <mark.j.abra...@gmail.com>
>>>>> wrote:
>>>>>
>>>>>> On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole <x.peri...@rug.nl>
>>>>> 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->x, state->natoms);
>>>>>> exchange_rvecs(ms, b, state->v, state->natoms);
>>>>>> exchange_rvecs(ms, b, state->sd_X, state->natoms);
>>>>>> }
>>>>>>
>>>>>> I mis-stated last night - there *is* exchange of ensemble data, but it
>>> is
>>>>>> incomplete. In particular, state->ekinstate is not exchanged. Probably
>>> it
>>>>>> is incomplete because the 9-year-old comment about t_state changing is
>>>>> in a
>>>>>> location that nobody changing t_state will see. And serializing a
>>>>> complex C
>>>>>> data structure over MPI is tedious at best. But that is not really an
>>>>>> excuse for the non-modularity GROMACS has for many of its key data
>>>>>> structures. We are working on various workflow and actual code
>>> structure
>>>>>> improvements to fix/prevent issues like this, but the proliferation of
>>>>>> algorithms that ought to be inter-operable makes the job pretty hard.
>>>>>>
>>>>>> Other codes seem to exchange the ensemble label data (e.g. reference
>>>>>> temperatures for T-coupling) because they write trajectories that are
>>>>>> continuous with respect to atomic coordinates. I plan to move REMD in
>>>>>> GROMACS to this approach, because it scales better, but it will not
>>>>> happen
>>>>>> any time soon.
>>>>>>
>>>>>> That would explain what I see, but let see what 4.5.7 has to say first.
>>>>>>>
>>>>>>
>>>>>> Great. It may be that there were other issues in 4.5.3 that exacerbated
>>>>> any
>>>>>> REMD problem.
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>> Tks.
>>>>>>>
>>>>>>> On Apr 25, 2013, at 22:40, Mark Abraham <mark.j.abra...@gmail.com>
>>>>> wrote:
>>>>>>>
>>>>>>>> Thanks for the good report. There have been some known issues about
>>> the
>>>>>>>> timing of coupling stages with respect to various intervals between
>>>>>>> GROMACS
>>>>>>>> events for some algorithms. There are a lot of fixed problems in
>>> 4.5.7
>>>>>>> that
>>>>>>>> are not specific to REMD, but I have a few lingering doubts about
>>>>> whether
>>>>>>>> we should be exchanging (scaled) coupling values along with the
>>>>>>>> coordinates. (Unlike most REMD implementations, GROMACS swaps the
>>>>>>>> coordinates, not the ensemble data.) If you can reproduce those kinds
>>>>> of
>>>>>>>> symptoms in 4.5.7 (whether or not they then crash) then there looks
>>>>> like
>>>>>>>> there may be a problem with the REMD implementation that is perhaps
>>>>>>> evident
>>>>>>>> only with the kind of large time step Martini takes?
>>>>>>>>
>>>>>>>> Mark
>>>>>>>>
>>>>>>>>
>>>>>>>> On Thu, Apr 25, 2013 at 1:28 PM, XAvier Periole <x.peri...@rug.nl>
>>>>>>> wrote:
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I have been recently using the REMD code in gmx-407 and gmx-453 and
>>>>> got
>>>>>>> a
>>>>>>>>> few systems crashing for unclear reasons so far. The main tests I
>>> made
>>>>>>> are
>>>>>>>>> using gmx407 but it is all reproducible with gmx453. The crashing
>>> was
>>>>>>> also
>>>>>>>>> reproduced (not necessarily at the same time point) on several
>>>>>>>>> architectures.
>>>>>>>>>
>>>>>>>>> The system is made of a pair of proteins in a membrane patch and for
>>>>>>> which
>>>>>>>>> the relative orientation is controlled by non-native
>>>>>>> bond/angles/dihedrals
>>>>>>>>> to perform an umbrella sampling. I use the MARTINI force field but
>>>>> that
>>>>>>>>> might not be relevant here.
>>>>>>>>>
>>>>>>>>> The crashes occur following exchanges that do not seem to occur the
>>>>>>>>> correct way and preceded by pressure scaling warnings … indicative
>>> of
>>>>> a
>>>>>>>>> strong destabilisation of the system and eventual explosion. Some
>>>>>>>>> information seems to be exchanged inaccurately.
>>>>>>>>>
>>>>>>>>> Trying to nail down the problem I got stuck and may be some one can
>>>>>>> help.
>>>>>>>>> I placed a pdf file showing plots of bonded/nonbonded energies,
>>>>>>>>> temperatures, box size etc … around an exchange that does not lead
>>> to
>>>>> a
>>>>>>>>> crash (here: md.chem.rug.nl/~periole/remd-issue.pdf). I plotted
>>> stuff
>>>>>>>>> every step with the temperature colour coded as indicated in the
>>> first
>>>>>>>>> figure.
>>>>>>>>>
>>>>>>>>> From the figure it appears that the step right after the exchange
>>>>> there
>>>>>>> is
>>>>>>>>> a huge jump of Potential energy coming from the LJ(SR) part of it.
>>>>>>> Although
>>>>>>>>> there are some small discontinuities in the progression of the bond
>>>>> and
>>>>>>>>> angle energy around the exchange they seem to fine. The temperature
>>>>> and
>>>>>>> box
>>>>>>>>> size seem to respond to it a few step latter while the pressure
>>> seems
>>>>>>> to be
>>>>>>>>> affected right away but potentially as the Epot will affect the
>>> viral
>>>>>>> and
>>>>>>>>> thus the Pressure.
>>>>>>>>>
>>>>>>>>> The other potential clue is that the jumps reduce with the strength
>>> of
>>>>>>> the
>>>>>>>>> pressure coupling. A 1/2 ps tau_p (Berendsen) will lead to a crash
>>>>>>> while a
>>>>>>>>> 5/10/20 ps won't. Inspection of the time evolution of the Epot, box
>>> …
>>>>>>>>> indicates that the magnitude of the jumps is reduced and the system
>>> ca
>>>>>>>>> handle the problem.
>>>>>>>>>
>>>>>>>>> One additional info since I first posted the problem (delayed by the
>>>>>>> file
>>>>>>>>> first attached but now given with a link) the problem is accentuated
>>>>>>> when
>>>>>>>>> the replicas differ in conformation. I am looking at the actual
>>>>>>> differences
>>>>>>>>> as you'll read this email.
>>>>>>>>>
>>>>>>>>> That is as far as I could go. Any suggestion is welcome.
>>>>>>>>>
>>>>>>>>> XAvier.
>>>>>>>>> MD-Group / Univ. of Groningen
>>>>>>>>> The Netherlands--
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