Re: AMBER: trajectory problem

From: David A. Case <>
Date: Wed, 7 Feb 2007 09:52:59 -0800

On Wed, Feb 07, 2007, Miguel Ferreira wrote:
> I am with a stupid problem. I run 1 ns simulation in 10 stages of 100 ps
> each. The problem is that I choose ntpr, ntwr and ntwx to be 300. Only now
> I notice that this gives a fractional number of frames per simulation, that
> is 166,7. So, the last frame is never written to the output files and the
> trajectory files cannot be correctly concatenated. I was thinking to strip
> the 166 frames of each stage and then concatenate the files.

It should be the case that the trajectory files would already have 166 frames
in them, and could be concatenated as they stand. The (minor?) problem
remaining would be that the time spacing between frames would be slightly
different at the ends of each of the 10 fragments. I don't see any way around
this problem other than to re-run (or extend) the simulation).

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Received on Sun Feb 11 2007 - 06:07:09 PST
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