[gmx-users] trjcat

[Tsjerk Wassenaar]

Hi Eric,

Your .mdp file has tinit = 0, so you reset the time. You will have started
from the structure in thev .cpt file though, which is what you want. You
can set the time whit trjcat, but you may have some overlapping frames in
the output.

Cheers,

Tsjerk

On Fri, Oct 31, 2014 at 8:18 PM, Eric Smoll <ericsmoll at gmail.com> wrote:

> Hello Gromacs users,
>
> I ran a 2 ns simulation (using "A.mdp" and "A.top") and obtained the files
> "A.trr," and "A.cpt," and "A.gro."
>
> I would like to continue the simulation over an identical interval with
> identical settings. I executed the following commands:
>
> grompp -f  A.mdp
>              -c  A.gro
>              -t  A.cpt
>              -f  A.top
>              -o  B.tpr
>
> mdrun -s  B.tpr
>            -o  B.trr
>            -c  B.gro
>            -e  B.edr
>            -g  B.log
>
> When I tried to concatenate the output with trjcat, I obtain
>
>           File                Start time       Time step
> ---------------------------------------------------------
>   A.trr        0.000 ps        0.400 ps
>   B.trr        0.000 ps        0.400 ps WARNING: same Start time as
> previous
>
> This warning is worrisome. Did I continue the trajectory incorrectly?
>
> Best,
> Eric
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-- 
Tsjerk A. Wassenaar, Ph.D.