I am doing a manual replica exchange(generalized hamiltonian rem) after every mdrun. If the replica exchange is successful, then I "exchange checkpoint files". For example, consider the following:
Simulation parameters:....................B1.........B2 Replicas(coordinates and velocities):.R1.........R2 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY) 1. Mdrun run - 500 steps = 1ps 2. Attempt exchange - NOT SUCCESSFUL 3. Exchange implementation: SKIP 4.Continue to next step ..... 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY) 1. Mdrun run - 500 steps = 1ps 2. Attempt exchange - If successful, exchange 3. Exchange Implemented by - exchanging checkpointing files 4. Continue to next step 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY) 1. Mdrun with exchanged .cpt files -NOW this is where the problem shows.. i) The log, xtc files are not appended when beginning after a step with a successful exchange attempt:*According to Mark's previous mail, this could be a result of mismatch in ensembles. Which means that the .cpt is ignored - implying that the mdrun in B1 DOES NOT start from R2.* Therefore, to make R1 run in B2 and R2 run in B1, do I need to supply .cpt to tpbconv instead of mdrun after a successful exchange step? To summarize: APPENDING HAS NOW BECOME A SECONDARY CONCERN, WHAT I AM INTERESTED IN IS A SUCCESSFUL MANUAL REPLICA EXCHANGE RUN AS POINTED OUT ABOVE. I hope my dilemma is clear now. Pooja On Tue, Feb 1, 2011 at 11:42 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Sai Pooja wrote: > >> From the website: >> "If you change the integrator or ensemble, you should pass the checkpoint >> file to tpbconv only, not to mdrun, since the state might change and thus >> output files can not be appended." >> >> > > Are you changing the integrator, ensemble, and/or other settings? If not, > this statement does not apply. For a simple -append after extending via > tpbconv, this is not applicable. > > > So now instead of supplying the checkpoint file to mdrun I supply it to >> tpbconv... does this assure that the simulations start from the >> coordinates/velocities specified by the .cpt file? >> >> > > For a simple extension, you do not pass the .cpt file to tpbconv. > > > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4 > > > Thanks Mark. So if the simulation doesn't start from the checkpoint >> file, from where are the initial coordinates velocities etc. taken >> from?... the trajectory files? >> > > Mark's previous message already answered this. > > -Justin > > Also, I could not find the environment variable... and I am not >> sure >> how to use one. >> Pooja >> On Tue, Feb 1, 2011 at 3:03 AM, Mark Abraham >> <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote: >> >> On 1/02/2011 7:50 AM, Sai Pooja wrote: >> >>> I think I have figured out the reason. It is because I am >>> carrying out replica exchange (manual) after every mdrun. If >>> the exchange occurs, I exchange the checkpoint files, extend >>> the simulation by 500 steps and continue. The new simulation >>> starts from exchanged cptfile. It seems that whenever the >>> exchange occurs, the earlier log,traj files are not appended. >>> They are instead overwritten. the obv solution is to save and >>> index these files with the relevant replicas everytime an >>> exchange occurs. >>> >> >> This would have been good to know earlier. If replica-exchange >> leads to the ensemble of the .tpr not matching the ensemble of >> the .cpt, then IIRC 4.5.3 mdrun will refuse to start from the >> .cpt, which means the subsequent mdrun will start from the .tpr >> only. Certainly a non-appending mdrun prints a warning (or >> error, I forget which) message to the log file, but perhaps the >> use of -append (erroneously) doesn't do that. Please have a look >> and see if that is the issue. There is an environment variable >> that can be set to tell mdrun that you (think you) know what you >> are doing mismatching .tpr and .cpt. >> >> Mark >> >> >> However, i have a more general question. Since mdrun still >>> runs with the exchanged checkpoint files and starts from the >>> point where the previous run ended, can I be assured that an >>> exchange has been affected - since tpr files correspond to the >>> "replica-box" and cpi to the most recent exchanged replicas? >>> Pooja >>> >>> On Mon, Jan 31, 2011 at 2:33 PM, Sai Pooja <saipo...@gmail.com >>> <mailto:saipo...@gmail.com>> wrote: >>> >>> >>> I manually index checkpoint files after every mdrun. What >>> troubles me is the randomness with which -append fails/works. >>> For eg, I have a simulation which runs from 3ns, >>> 1ps in 1 >>> mdrun. Now oddly enough, the logfile starts from 1184ps(in >>> the end, I do remember the one starting from 0 but that >>> was overwritten it seems) and the rest is appended uptil >>> the 3000ps step. Why would append work from 1184ps to >>> 3000ps but not for the previous ones?Could it have >>> anything to do with the network/cluster? If that is the >>> case is it safer to create a new file everytime and then >>> concatenate them after say every 100ps? >>> Pooja >>> On Sat, Jan 29, 2011 at 6:52 PM, Mark Abraham >>> <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> >>> >>> wrote: >>> >>> On 30/01/2011 10:39 AM, Sai Pooja wrote: >>> >>>> I would be happy to supply more information.. if >>>> someone could please look into this.. otherwise I >>>> will have to switch to storing every file and then >>>> just concatenating them which seems like a rather >>>> roundabout way of doing it. >>>> >>> >>> As I suggested a few emails ago, are you sure that >>> -cpi file exists? If your numerical suffixes are >>> indexing restarts, then unless you've done some manual >>> copying that you haven't told us about, it won't. Your >>> filename scheme seems a bit contorted - like you're >>> trying to do the work that GROMACS 4.5.x will just do >>> for you if you let it. >>> >>> Otherwise, you'll have to do some detective work with >>> gmxcheck on the -cpi to see what might be the issue. >>> >>> In your case, an initial >>> >>> mdrun -deffnm rex_3 >>> >>> (perhaps save some copies while you're experimenting) >>> and subsequently >>> >>> tpbconv -extend <blah> -f rex_3 -o rex_3 >>> mdrun -deffnm rex_3 -append >>> >>> will work and be much simpler than whatever you're >>> trying to do with filenames :-) >>> >>> Mark >>> >>> >>> >>>> On Fri, Jan 28, 2011 at 4:37 PM, Sai Pooja >>>> <saipo...@gmail.com <mailto:saipo...@gmail.com>> wrote: >>>> >>>> This is the command: >>>> nbs submit -command >>>> "(/usr/local/gromacs/4.5.1/bin/mdrun_mpi -s >>>> rex_3.tpr -e rex_3 -c after_rex_3 -cpi restart3 >>>> -cpo restart3 -ap >>>> pend -g rexlog3 -x rextraj3);" -nproc 1 -name >>>> "GENHAM-DIHEDRAL-3" -mail start end >>>> Pooja >>>> >>>> On Fri, Jan 28, 2011 at 4:20 PM, Mark Abraham >>>> <mark.abra...@anu.edu.au >>>> <mailto:mark.abra...@anu.edu.au>> wrote: >>>> >>>> On 29/01/2011 3:56 AM, Sai Pooja wrote: >>>> >>>> Hi, >>>> I am using tpbconv and mdrun to extend a >>>> simulation. I use it with the append >>>> option but the files still get >>>> overwritten or erased. Can someone help >>>> me in this regard? >>>> Pooja >>>> Commands (in python) >>>> cmd = '(%s/tpbconv -extend %f -s >>>> rex_%d.tpr -o rex_%d.tpr)' >>>> %(GROMPATH,dtstep,i,i) >>>> os.system(cmd) >>>> time.sleep(1) >>>> cmd = 'nbs submit -command "' >>>> cmd += '(%s/mdrun_mpi -noh >>>> -noversion -s rex_%d.tpr -e rex_%d -c >>>> after_rex_%d -cpi restart%d -cpo >>>> restart%d -append -g rexlog%d -x >>>> rextraj%d >/dev/null); ' >>>> %(GROMPATH,i,i,i,i,i,i,i) >>>> cmd += '" ' >>>> cmd += '-nproc 1 ' >>>> cmd += '-name "GENHAM-DIHEDRAL-%d" '%(i) >>>> cmd += '-mail start end ' >>>> cmd += '-elapsed_limit 16h >> rexid' >>>> os.system(cmd) >>>> >>>> >>>> More useful for diagnostic and >>>> record-preservation purposes is to construct >>>> the cmd string and print it to stdout (or >>>> something). >>>> >>>> At the moment it is far from clear that your >>>> -cpi file exists for the new run. >>>> >>>> Mark >>>> -- gmx-users mailing list >>>> gmx-users@gromacs.org >>>> <mailto:gmx-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 >>>> <mailto:gmx-users-requ...@gromacs.org>. >>>> >>>> Can't post? Read >>>> http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> >>>> >>>> >>>> -- Quaerendo Invenietis-Seek and >>>> you shall discover. >>>> >>>> >>>> >>>> >>>> -- Quaerendo Invenietis-Seek and you >>>> shall discover. >>>> >>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-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 >>> <mailto:gmx-users-requ...@gromacs.org>. >>> >>> Can't post? Read >>> http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >>> >>> -- Quaerendo Invenietis-Seek and you shall >>> discover. >>> >>> >>> >>> >>> -- Quaerendo Invenietis-Seek and you shall discover. >>> >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- Quaerendo Invenietis-Seek and you shall discover. >> >> >> >> >> -- >> Quaerendo Invenietis-Seek and you shall discover. >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 gmx-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 > -- Quaerendo Invenietis-Seek and you shall discover.
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