[gmx-users] mdrun with append option

[Sai Pooja]

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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