[gmx-users] extending npt step/generating output from crashed/fatal error-based quit session.

Justin Lemkul jalemkul at vt.edu
Tue Apr 5 15:25:05 CEST 2016

On 4/5/16 8:29 AM, David Newman wrote:
> While running the npt step gromacs encountered the following error about 4-6ps before the end of the mdrun:
> File input/output error:
> npt_step46830.cpt
> I tried the commands for extending the simulation but these seem setup for the production runs as it quite complaining about the lack of topol.tpr, is there a way to either output what I need for the production run from what I have or a set of commands that allow me to finish the crashed sim?

Add -cpi -append to whatever your previous command was.  The error you're 
getting regarding topol.tpr means you're not specifying any input file names, so 
the defaults are used.



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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