[gmx-users] after extending simulation

Andrea Spinelli 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
> 
> -- 
> ==================================================
> 
> 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
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==================================================
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

Andrea Spinelli

Please do not print this email unless really need to.
Save paper, save trees, save space, save money - life matters.



More information about the gromacs.org_gmx-users mailing list