[gmx-users] mdrun with append option

Mark Abraham Mark.Abraham at anu.edu.au
Wed Feb 2 00:48:50 CET 2011


On 2/02/2011 3:38 AM, 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."

Where was that? It could use clarification.

Mark

> 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?
> Pooja
>
> On Tue, Feb 1, 2011 at 11:20 AM, Sai Pooja <saipooja at gmail.com 
> <mailto:saipooja at gmail.com>> wrote:
>
>     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.Abraham at anu.edu.au <mailto:Mark.Abraham at 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
>>         <saipooja at gmail.com <mailto:saipooja at 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.Abraham at anu.edu.au
>>             <mailto:Mark.Abraham at 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
>>>                 <saipooja at gmail.com <mailto:saipooja at 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.Abraham at anu.edu.au
>>>                     <mailto:Mark.Abraham at 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
>>>                         -- 
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>>>
>>>
>>>
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>>
>>
>>                 -- 
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>>
>>
>>
>>         -- 
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>
>
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