[gmx-users] doing restarts

Justin A. Lemkul jalemkul at vt.edu
Sun Sep 11 03:03:10 CEST 2011

Juliette N. wrote:
> Hello,
> I am trying to extend a simulation to 2 ns and wanted to know if I am 
> using the proper tools for this purpose. (version 4.5.4)
> 1) tpbconv –f old.trr -s old.tpr –e old.edr -o old-extend.tpr -until 2000
> mdrun -s old-extend.tpr  -cpi old.cpt   -o old-extend  -c old-extend -e 
> old-extend
> Is what I am doing correct?

Yes.  Save yourself some typing with:

mdrun -deffnm old-extend -cpi old.cpt

> 2) Can I use the following in 4.5.4 instead of above?
> mdrun -s old.tpr -cpi old.cpt -append 2000

No.  The mdrun -append option does not take an argument; it is a boolean (i.e. 
-append/-noappend) to indicate whether old files are to be appended to or not.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list