AMBER Archive (2008)

Subject: Re: AMBER: Running Amber8 - Sander

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon Dec 01 2008 - 09:37:32 CST

On Mon, Nov 24, 2008, tri nam Vo wrote:

> I'm using Amber8 for simulate my protein at const pH. I'd like to run
> 500.000 step with dt=0.002 (total 1ns). Because of not good electric power,
> I'd like to run sander in separated period with 10.000 steps in each
> period. The results are different between running in multi period with
> running in one time with 500.000 steps.
> The question is why there is this difference? Can I use the result in
> multi-period running?

You should be able to do what you propose. Be aware that there has been a
report of restart problems with constant pH and parallel simulation. Run some
short tests to be sure that doing a longer calculations matches what you get
with two shorter calculations.

...dac

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