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

From: Jason Swails <>
Date: Sat, 19 Oct 2013 09:13:56 -0400

On Fri, Oct 18, 2013 at 7:23 PM, <> wrote:

> Hi Daniel,
> I have one more question that popped into my head while thinking about
> doing this.
> How do I determine the number of frame where the simulation crashed? The
> mdcrd (traj1) will have information till frame Y. So in that case, how do I
> determine X?
> Once I determine X, I can do as you suggested and read 1 to X frames of
> traj1 and then read in traj2 (starting from X) and combine the both.

Look at the time. The time is the second number on the second line of the
restart file you used. Match that up with the time in the mdout file to
figure out what step the restart corresponds with. Along with the total
number of frames in your first trajectory, that will tell you what you want
to know.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sat Oct 19 2013 - 06:30:02 PDT
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