[gmx-users] after extending simulation

Justin Lemkul jalemkul at vt.edu
Thu Jul 9 19:38:31 CEST 2015

On 7/9/15 1:25 PM, Andrea Spinelli wrote:
> Dear all,
> I extend a simulation (GROMACS 5.0.5) with these command lines:
> convert-tpr -s md_0_1.tpr -extend 1000 -o next.tpr
> mdrun -s md_0_2.tpr -cpi md_0_1.cpt
> And now?

Well, the above sequence of commands won't do anything because (1) it's "gmx 
convert-tpr" not just "convert-tpr" and (2) if you create "next.tpr" and try to 
run "md_0_2.tpr" then mdrun will exit.

> What I have to do to view the new .gro file (i use VMD to see it) with new state of protein folding simulation?

Load it like any coordinate file.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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