Re: [AMBER] Rewrapping restart file

From: Daniel Roe <>
Date: Mon, 8 Sep 2014 10:51:09 -0600


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,


On Mon, Sep 8, 2014 at 10:08 AM, Geoffrey Gray <> 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

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Sep 08 2014 - 10:00:02 PDT
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