[gmx-users] restarting mdrun

[Chandan Choudhury]

Hi Mark !!!
Thanks for answering.
My query is how do I restart my mdrun because the command
nohup mpirun -np 16 -machinefile mac mdrun -s md5-10.tpr -cpi state.cpt
-append &
will not start from where the trajectory was stopped (i.e; time 9169.500).
As this command will continue the simulation from where the cpt file was
written.

Any suggestions??

chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Tue, Feb 16, 2010 at 9:36 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 17/02/10 02:52, Chandan Choudhury wrote:
>
>> Hello gmxusers !!!
>> I want to continue my simulation, from where the point where it stopped.
>> The gmxcheck on .trr and cpt files are as:
>>
>> $gmxcheck -f state.cpt
>>
>> Checking file state.cpt
>>
>> # Atoms  186864
>> Last frame         -1 time 9362.500
>>
>>
>> Item        #frames Timestep (ps)
>> Step             1
>> Time             1
>> Lambda           1
>> Coords           1
>> Velocities       1
>> Forces           0
>> Box              1
>>
>> $gmxcheck -f 5-10.trr
>>
>> Checking file 5-10.trr
>> trn version: GMX_trn_file (single precision)
>> Reading frame       0 time 5169.500
>> # Atoms  186864
>> Reading frame    8000 time 9169.500
>>
>>
>> Item        #frames Timestep (ps)
>> Step          8395    0.5
>> Time          8395    0.5
>> Lambda        8395    0.5
>> Coords        8395    0.5
>> Velocities    8395    0.5
>> Forces           0
>> Box           8395    0.5
>>
>>
>> There is a mismatch of time in both the outputs.
>>
>> The date of modification of both the files as shown are:
>>
>> Feb 15 19:55 state.cpt
>>
>> $date -r 5-10.trr
>> Mon Feb 15 19:59:56 IST 2010
>>
>> The cpt file shows time greater than the trr file. But the time of
>> modification of cpt file is less than trr file.
>>
>
> If the simulation stopped catastrophically, then the timestamp could easily
> differ, especially if the .cpt is opened, written to and closed
> periodically, and the .trr is open continuously.
>
>
>  Cannot understand the,
>> how to restart the mdrun. And the size of the trr file is 36GB. Can I
>> use the append flag in mdrun for gmx 4.0.5.
>>
>
> Search the webpage for suggestions.
>
> Mark
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