[gmx-users] omit solvent's coordinates in output file

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 25 17:23:38 CET 2010

vedat durmaz wrote:
> dear gromacsters,
> does anyone know a way to tell gromacs which molecule's coordinates to
> write to the output file which should be as small as possible? i don't
> need the solvent's coordinates for example.
> starting run like:
> grompp -f ../../md.mdp -c eq.gro -n index.ndx -p complex.top -o md.tpr
> mpiexec -n 32 mdrun -v -deffnm md 2>&1
> thanks a lot and best regards

See the "xtc_grps" keyword in the .mdp file.  This will have no effect on the 
output coordinate file, but will keep the .xtc trajectory small(er).  It also 
has no effect on your .trr file, so choose nstxout, nstvout, etc appropriately.


> vedat


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


More information about the gromacs.org_gmx-users mailing list