[gmx-users] mdrun with append option
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 1 17:42:21 CET 2011
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.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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--
========================================
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
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