Re: [AMBER] combining coordinate and velocity files into one

From: Jason Swails <>
Date: Sun, 7 Mar 2010 17:48:23 -0500


On Sun, Mar 7, 2010 at 4:42 PM, Amire-Brahimi Benjamin
<> wrote:
> Hi there guys,
> Is there any way to combine these files into one? I am trying to restart an
> MD simulation, but when I change irest from 0 to 1 I must also change the

Restarting a simulation should be done with the restart file. Any
restrt file created during an MD trajectory has both coordinates and
velocity information printed to it. Any other restrt file created
(i.e. by leap or a minimization) does not (as there are no velocities
associated with it). Trajectory files written out via the ntwx and
ntwv parameters are primarily there for analysis, and should not be
used to restart runs.

The restrt file is specified by the "-r restrt" flag for both pmemd
and sander. If you did not specify this flag during the simulation,
then "restrt" is the default name. Again, if you are not restarting
from an MD simulation, then there will be no velocity information in
the restart file and you will have to set irest=0, ntx=1 for that
simulation (using the previous restrt file as the inpcrd file under
the -c flag). Otherwise, use irest=1, ntx=5. The other values for
ntx are for unformatted files that would be created by different
programs, for example (they are not commonly used).

Hope this helps,

> value for ntx. I have tried all of the values from 1 to 7 using separate
> velocity and trajectory files. The error FATAL: Could not read velocities
> from min_chaina_gol.crd  seems to suggest I need one solitary file.
> Thanks,
> Ben
> --
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Sun Mar 07 2010 - 15:00:03 PST
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