Re: [AMBER] Question about the influence of trajectory format (ioutfm) on results - part 2

From: David A Case <>
Date: Wed, 1 Jun 2011 12:30:07 -0400

On Wed, Jun 01, 2011, Lorenzo Gontrani wrote:

> I need to map exactly the coordinates to the velocities for each frame
> (I have to run new simulations - with different parameters - starting
> from "hot" frames, that have given structural patterns, and study the
> time decay of such patterns eith shorter timesteps).
> I intended to do it with ptraj, dumping coordinates (from mdcrd) and
> velocities (from mdvel) and then combining them into hot restart
> files.

This won't work. What you want to do is to set ntwr to a negative number (see
the manual). Then you will get "true" restart files at whatever interval you

...good luck...dac

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Received on Wed Jun 01 2011 - 10:00:03 PDT
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