[gmx-users] mdrun with append option

Sai Pooja saipooja at gmail.com
Tue Feb 1 17:20:08 CET 2011 

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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>>>>
>>>>
>>>>
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>>>>
>>>
>>>
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>
>
>
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