[gmx-users] after extending simulation
jalemkul at vt.edu
Thu Jul 9 19:58:34 CEST 2015
On 7/9/15 1:49 PM, Andrea Spinelli wrote:
> 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?
The contents of md_0_1.tpr and md_0_2.tpr are identical except that the latter
contains a different number of steps. When providing mdrun with a .cpt file, it
carries out the run from that point, so the starting point of the run (time = 0)
is always the same.
The final coordinates are always written to a .gro file unless you specify a
different format (which your above command does not). Whatever that file is
called depends on the first run (md_0_1), because the file names are stored in
the .cpt file; they will be appended to by default. The final .gro file has an
appended name rather than being overwritten, IIRC.
> 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
>> 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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> Andrea Spinelli
> Please do not print this email unless really need to.
> Save paper, save trees, save space, save money - life matters.
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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