[gmx-users] after extending simulation

[Andrea Spinelli]

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
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
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> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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Andrea Spinelli

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