[gmx-users] restarting mdrun

[Chandan Choudhury]

Thanks Justin !!
But my state_prev.cpt file shows
$gmxcheck -f state_prev.cpt

Checking file state_prev.cpt

# Atoms  186864
Last frame         -1 time 9346.700


Item        #frames Timestep (ps)
Step             1
Time             1
Lambda           1
Coords           1
Velocities       1
Forces           0
Box              1

Here also the time is greater than the .trr file.

Cant understand how to overcome it.

Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Tue, Feb 16, 2010 at 11:02 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Chandan Choudhury wrote:
>
>> 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.
>>
>>
> Right, it will start from whenever the checkpoint was written.  You should
> also have a state_prev.cpt that is a backup in case this type of thing
> happens; it may help.  Regardless, with a 36-GB .trr file, the -append
> option will not work.  Leave it out and use trjcat later.
>
> -Justin
>
>  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<mailto:
>> 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
>>    --    gmx-users mailing list    gmx-users at gromacs.org
>>    <mailto:gmx-users at gromacs.org>
>>
>>    http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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