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?
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>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> 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>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> 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 >>>> > 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 >>>>> 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. >>>> >>> >>> >>> >>> -- >>> Quaerendo Invenietis-Seek and you shall discover. >>> >>> >>> >>> -- >>> >>> 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. >> > > > > -- > Quaerendo Invenietis-Seek and you shall discover. > > > > -- > 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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