[gmx-users] rerun on gro file

Justin A. Lemkul jalemkul at vt.edu
Sat Sep 18 20:21:13 CEST 2010

fahimeh baftizadeh wrote:
> Hi,
> I'm trying to do rerun on a trajectory which came from catting some gro 
> files of a metadynamics simulation. I simply did trjcat -f 1.gro 2.gro 
> 3.gro -o all.xtc -cat
> then I used this all.xtc for rerun.
> the output COLVAR is written but only for one step, I did test on some 
> other trajectory and I am sure that META_INP.dat which is the input of 
> metadynamics is correct.
> I dont know if the problem is catting the gro file ?!!

Probably.  Use -settime to assign times to each of the frames, otherwise they 
may all be set to something like 0 or -1.  You can use gmxcheck on the .xtc file 
to see what Gromacs thinks it contains.


> Fahimeh 


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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