Re: [AMBER] STOP PMEMD Terminated Abnormally!

From: David A Case <>
Date: Mon, 17 Aug 2015 07:51:55 -0400

On Mon, Aug 17, 2015, Pragya Priyadarshini wrote:
> I am doing MD simulation of Protein-DNA complex for total 80 ns. I have
> been using iwrap=0 for all the production run and it worked fine till
> 50ns . while extending simulation run after 50ns it is unable to read
> restart file. By the help of Amber mailing list I came to know that for
> long run MD simulation iwrap=1 should be use.
> Now I am running MD with iwrap=1, though it is reading the restart file
> I am concerned that if it could affect the calculation during next MD
> run.

What you describe should be fine. But we recommend using netCDF format for
both restart and trajectory files: set ioutfm=1 and ntxo=2.


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Received on Mon Aug 17 2015 - 05:00:07 PDT
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