Re: [AMBER] How to deal with duplicate frames during MD?

From: Daniel Roe <>
Date: Fri, 18 Oct 2013 07:59:42 -0600


On Fri, Oct 18, 2013 at 2:34 AM,
<> wrote:
> Now, if I restart my MD using this rst file, it will again write the frames
> which are already in the previous trajectory (till the point where it
> crashed i.e. Y) and then proceed to write the rest.

Be aware this is not necessarily true depending on what kind of
simulation you are doing. In particular if you are using the Langevin
thermostat the random number stream will be different, so the
trajectory of your restarted run from X to Y will probably not match
the previous run from X to Y.

> My question is, while using ptraj to combine these two trajectories, how
> can I make sure that the duplicate frames are written only once? Is there a
> flag I can use, maybe something similar to -overwrite flag in
> gromacs?

You can do this in cpptraj/ptraj by specifying appropriate frame
ranges to your trajin argument. For example, say your first trajectory
crashed at frame 105 and you are restarting from frame 100 (assuming
the second traj didnt crash as well):

trajin traj1 1 100
trajin traj2
trajout combined

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Oct 18 2013 - 07:00:17 PDT
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