[gmx-users] Extending simulation problem.

[Dawid das]

Well in my *log file nothing about state or *cpi files is mentioned.
Acutally I have a question regarding state.cpi files. Does it contain names
of *gro, *trr, etc. files if they are not standard?
The thing is, that output files from my first 5ns simulation are not
standard. Now, I perform these calculations not in my working directory but
on separate scratch.
In this case, should the output files from previous simulation be present
in the scratch?
And when I run another 5 ns should I run mdrun with those -c -o and -e
options? If yes, should the names of files be the same as in the previous
simulation?


2014-08-20 18:18 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 8/20/14, 6:33 AM, Dawid das wrote:
>
>> Dear Gromacs experts,
>>
>> I googled for answer and I found these:
>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>> http://www.researchgate.net/post/How_to_extend_the_
>> protein_simulation_in_Gromacs_from_1000_ps_to_10000_ps
>>
>> but still I am confused about what happens in my simulation. I did 5 ns
>> simulation and I would like to add extra 5 ns on top of that so that new
>> results (energies, temperature, trajectory, etc.) will be appended to
>> already existing files after first 5 ns simulation. Now I used this
>> command
>> to run MD simulation for the first time:
>>
>> \$MDRUN -v -s npt-md.tpr -o mCherry7-npt-md.trr -c mCherry7-npt-md.gro -e
>> mCherry7-npt-md.edr > $CURDIR/mCherry7-npt-md.log 2>&1
>>
>> After this in the same directory I run:
>>
>> tpbconv -s npt-md.tpr -extend 5000 -o npt-md-ext.tpr
>> \$MDRUN -s npt-md-ext.tpr -cpi state.cpt
>>
>> I tried both state.cpt and prev_state.cpt and the beginning of new
>> simulation looks exactly the same
>>
>> that means temperature, energies, etc. are the same as if I started
>> from 0ns step, not from 5ns step of
>>
>> previous simulation. What can cause that? Is it because of used files
>> names or I did something else wrong?
>>
>>
> What does the .log file say?  It should clearly indicate if the restart
> was done by reading in the checkpoint file.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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