Awesome, thank you very much! I just wanted to confirm that there was not a
bug I was unaware of and the velocities were being modified.
Thanks again,
Geoffrey
On Mon, Sep 8, 2014 at 12:51 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> The restart time is the only thing modified by cpptraj (it's set to
> the frame number). This was originally done since some coordinate
> formats don't really have a concept of time (and indeed cpptraj
> doesn't really make use of the time field). This behavior will
> probably be changed in future releases. For now, if you want to
> explicitly set the time value of a restart you can use the 'time0'
> keyword with 'trajout'.
>
> Hope this helps,
>
> -Dan
>
> On Mon, Sep 8, 2014 at 10:08 AM, Geoffrey Gray <gmgray2.mail.usf.edu>
> wrote:
> > Good afternoon: I am running simulations using a truncated octahedron
> water
> > box. I do not wrap the water during the simulation ( iwrap=0 ), however I
> > do rewrap the restart file using cpptraj and the following input script:
> >
> > ############
> > parm prmtop/mut.prmtop
> > trajin data/md2.rst7
> >
> > autoimage origin
> >
> > trajout data/md2-recenter.rst7
> > ############
> >
> > When looking at the input file, I notice that the cumulative time is
> > incorrect after I rewrap (i.e. the begin time read by Amber is 1 ps),
> > despite the fact that I set the flags to read in coordinates and
> velocities
> > for restarting. I wanted to confirm that the rewrapping is not affecting
> > the velocities for restart. If I do not rewrap, then the begin time is
> read
> > normally. I checked and the file sized of the unwrapped and rewrapped
> > restart files are the same, so all of the information should be there.
> > Thanks in advance!
> >
> > Geoffrey
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Sep 08 2014 - 11:30:03 PDT
