[gmx-users] Extending simulations

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 17 14:23:16 CET 2010

Milan Melichercik wrote:
> On Wednesday 17 March 2010 13:53:03 Carla Jamous wrote:
>> Hi everyone,
>> It's the first I use the process of extending simulations.
>> I did the following:
>> tpbconv -s prot.tpr -extend 6000 -o protein.tpr
>> mdrun -v -s protein.tpr -cpi state.cpt -cpo state_a.cpt -o protein.trr -c
>> protein.gro -x protein.xtc -e md.edr -g md.log
>> But I noticed sthg strange: gromacs named my files:
>> protein.part0002.gro/.xtc/.trr/.log/.edr
>> Please does anyone know why it did this?
>> Thanks
>> Carla
> This is OK - if you don't use "-append" in mdrun command, it will produce 
> another files as the continuation of the simulation - and the "partxxxx" is 
> just to have the order in them. At the end, you can use eneconv and trjcat to 
> get it in one peace.

If you don't want the "partxxxx" to appear in the filename, supply the 
-noaddpart flag to mdrun, but yes, this is quite normal.


> Milan


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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