[gmx-users] after extending simulation
spinelli87 at gmail.com
Thu Jul 9 19:49:04 CEST 2015
I’m sorry, I miss something with cut and paste command.
On terminal I wrote:
gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr
gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt
There is no gromacs coordinate file in VMD, I have to convert a md_0_2.tpr into try or try file?
On Jul 9, 2015, at 7:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
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