[gmx-users] Extended trajectory

[Arik Cohen]

Thanks allot for all your help

Arik

Justin A. Lemkul wrote:
>
>
> Arik Cohen wrote:
>> Hi,
>>
>> I'll be most thankful if someone could tell me how to run a 
>> fragmented trajectory using only the mdrun command. As of now I'm 
>> using :
>>
>> while(SimuTime < SimTime)
>>    {
>>       ...
>>     system("tpbconv -s run.tpr -f run.trr -e run.edr -extend 1.0 -o 
>> run.tpr");
>>     system("mdrun -cpi run.cpt -cpo run.cpt -append -npme 0 -v 
>> -deffnm run");
>>     ....
>>    }
>>
>> When I ran the above mdrun command alone, the run got stack
>>
>
> No error message?  Just stuck?  It could be that you're trying to read 
> and write to the same file names.  I think your method of preparing 
> the extended run is also malformed, since the advent of checkpoint 
> files.  See here:
>
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>
> Try with the syntax and naming convention given there (to avoid 
> potential I/O confusion) and see if your run works.
>
> -Justin
>
>> Thanks
>>
>> Arik
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