[gmx-users] trjcat

[Tsjerk Wassenaar]

Hi Eric,

Indeed. But the .cpt file contains the last frame from the first part,
which is then also the first frame of your last part, so you have it twice
in the output trajectory.

Cheers,

Tsjerk

On Fri, Oct 31, 2014 at 8:51 PM, Eric Smoll <ericsmoll at gmail.com> wrote:

> 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
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> >
> > --
> > Naga Rajesh Tummala
> > Post-Doctoral Researcher
> > Georgia Institute of Technology
> > email: nagarajesh at gatech.edu
> > ph: 405-200-7208
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Tsjerk A. Wassenaar, Ph.D.