[gmx-users] About extend the run,,

rama david ramadavidgroup at gmail.com
Sat Jun 2 17:51:09 CEST 2012

 Thank You  for Quick reply Justin...

On Sat, Jun 2, 2012 at 8:58 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> You'll get a mismatch in your files (checkpoint, trajectory, energy) in
> terms of frame interval.  You should not try to append to these files or
> extend the run.  Just run a new simulation from 20 -> 30 ns.  The grompp
> command was correct, assuming you set "tinit = 20000" in the .mdp file and
> setting nsteps appropriately to give another 10 ns.  Then run it as a new
> simulation.  It will still be an extension of the first simulation (since
> the .cpt preserves the previous state), but without the mdrun -cpi -append
> mechanism, which in this case you don't want (or possibly can't use)

I will follow your advice..

>         Second query;
>>        To rerun the crash run, users give .cpt file as input to -mdrun,
>>        My query is, There are two cpt file a) pre.cpt  b) .cpt ,
>>        So which one has to given as input???
>>    Use gmxcheck to understand the contents of each.  The timestamp will
>> also
>>    tell you a difference, as will reading mdrun -h for an explanation of
>> what
>>    the -cpt option is doing
>> As per the link..http://www.gromacs.org/**Documentation/File_Formats/**
>> Checkpoint_File<http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File>
>> I interpreted following things..
>> 1. I have to use the state.cpt , but in the case  problem to these I have
>> to use
>> prev.cpt,  I can check there
>>     content by gmxcheck..
>>      But my Query is What are may be the potential problems ?? and how to
>> find
>> them ??
>> Crash the run is very often with my system, that why I am worried..
> If you're getting frequent crashes, you should investigate why this is
> happening rather than just plowing ahead.  Are there error messages in the
> .log or stdout/stderr output?  Are your energetic terms sensible?  If the
> system is crashing due to physical instability, you're wasting your time
> producing junk. If the crashes are occurring due to hardware or filesystem
> instability, that's something to take up with your sysadmin.
> -Justin
Thank you For Advice...
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