[gmx-users] confusion about trjconv

Justin A. Lemkul jalemkul at vt.edu
Sun May 9 17:12:22 CEST 2010

shahid nayeem wrote:
> Dear all
> when I do long mdrun and the run crashes, I generate new .tpr file to
> restart the run. Sometime in order to complete run two or three such
> .tpr file is generated after reading previous .trr and .ene files.
> After completion of the run when I use trjconv (after combining .trr
> files with trjcat) which .tpr file should be used with -s flag the

That depends on what you're trying to use trjconv for, but probably the first 
.tpr file is what you want, since it would have been for the entire simulation 
if you had not had problems, right?

> first .tpr file which is generated with grompp at the start of mdrun
> or the last .tpr file generated by tpbconv reading previous .trr and
> .ene file. I know that in recent version of gromacs restart can be
> done using mdrun supplying .cpt file with -cpi flag. I require answer
> of my question regardless of the use of .cpt file.

Well, using the checkpoint mechanism is the more accurate (and easy!) way to go, 
so I don't know why you didn't use this feature...


> shahid nayeem


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


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