[gmx-users] trjcat

[Eric Smoll]

Hello Naga and Tsjerk,

Thank you for responding so rapidly. It is greatly appreciated.

A.mdp is not my first input file. It has the settings:
continuation=yes
gen-vel=no

I did not set tinit in "A.mdp." That is my problem. running "trjcat" with
"--settime" I set the first file to 0 and the second time to the special
option "c."  According to trjcat, "c" means "the start time is taken from
the end of the previous file. Use it when your continuation run restarts
with t=0." This seems correct.

Best,
Eric

On Fri, Oct 31, 2014 at 1:26 PM, Naga Rajesh Tummala <nagarajesh at gatech.edu>
wrote:

> 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
> --
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