[gmx-users] trjcat

[Naga Rajesh Tummala]

Hi Eric,

Did you change the tinit in A.mdp ? If you did not the initial time is same
in both A.xtc and B.xtc, one way to circumvent this is use -settime in
trjcat command.

And if A.mdp is your first input file, make sure to set velocity generation
to no upon restart so that B is an extension of A.

Best
Rajesh

On Fri, Oct 31, 2014 at 3:18 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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-- 
Naga Rajesh Tummala
Post-Doctoral Researcher
Georgia Institute of Technology
email: nagarajesh at gatech.edu
ph: 405-200-7208