AMBER Archive (2006)

Subject: Re: RE: Re: AMBER: A question about Dynamics.

From: David A. Case (
Date: Fri Sep 22 2006 - 19:57:46 CDT

On Fri, Sep 22, 2006, Qingning Shu wrote:
> At the beginning of second simulation, even
> the temperature dropped.

First run:
> sander -O -i -p vac.prmtop -c vac_min.rst -x vac_md0.crd -r
> vac_md0.rst -o vac_md0.out -ref vac_min.rst

Second run:

> sander -O -i -p vac.prmtop -c vac_md0.rst -x vac_md1.crd -r
> vac_md1.rst -o vac_md1.out -ref vac_md0.rst

You are using different restraint files for the two runs, so of course the
energies will differ. Take Ross Walker's advice, and try *short* runs with
ntpr=1. That is always a good idea when you results you don't understand.
Only printing every 20 steps makes debugging or understanding what is going on
very difficult.


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