[gmx-users] mdrun with append option

[Sai Pooja]

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.
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.
>



-- 
Quaerendo Invenietis-Seek and you shall discover.
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