[gmx-users] mdrun with append option

Sai Pooja saipooja at gmail.com
Tue Feb 1 17:38:00 CET 2011 

>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."

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



-- 
Quaerendo Invenietis-Seek and you shall discover.
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