Re: [AMBER] Creating a restart file from a trajectory file

From: David A Case <>
Date: Tue, 21 Jan 2014 07:42:12 -0500

On Tue, Jan 21, 2014, Ahmed Ayoub wrote:
> I have a trajectory mdcrd file for a long simulation that I have run
> before. I wanted to used the last snapshot in this simulation as a starting
> point for another simulation run. However, as far as I know, trajectory
> file don't contain velocity data and hence ptraj will not be able to print
> a restart file with velocities. Is this true?
> If yes, then the only solution is to heat the system and equilibrate it
> once more before the production run. Is this right?

You don't have to "heat it" again: just set the initial temperature to the
one you want, and continue the simulation.

(This is exactly what the Andersen (ntt=2) thermostat does at given


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Received on Tue Jan 21 2014 - 05:00:03 PST
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