[gmx-users] problem in extending MD in Gromacs 2018

Justin Lemkul jalemkul at vt.edu
Tue Oct 16 00:43:57 CEST 2018

On 10/15/18 5:34 PM, Ladan Mafakhe wrote:
> Hi
> I use Gromacs 2018. I ran one of my MD run. after finishing my MD I want to extend my PDB. I used these command as you say in Gromacs documentation2018. but my MD run did not extend and it started from the first step. why this happened and how I can fix it. the commands that I used:
> gmx convert-tpr -s md_0_1.tpr -o md-ex.tpr -until 40000
> gmx mdrun -v -s md-ex.tpr -e md-ex.edr -c md-ex.gro -o md-ex.trr -g md-ex.log

You're not getting a continuation because you're not asking for one. You 
need to use the -cpi flag and supply the name of the input .cpt file. 
Two other issues:

1. Save yourself some typing and use -deffnm
2. You can't change file names while trying to append to existing files 
(-append is the default behavior of mdrun)

So what you need is:

gmx mdrun -deffnm md-ex -cpi md_0_1.cpt -noappend



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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