Re: [AMBER] Query about microsecond long simulation

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 29 Apr 2015 09:57:16 -0400

> On Apr 29, 2015, at 9:53 AM, Ahmed Ezat <ezat.sci.cu.edu.eg> wrote:
>
> I am sorry but my question is out of this subject.
>
> 5ns windows means dividing the simulation in steps each 5ns or not.

Yes.

> What is meant by this " set ig=-1 here so that the random number seed
> changes automatically on every step otherwise you will get unrealistic
> correlations in your results.”?

This has to do with the well-described “Langevin Synchronization” effect. See it described here: http://www.ncbi.nlm.nih.gov/pubmed/11415160 <http://www.ncbi.nlm.nih.gov/pubmed/11415160> and here: http://pubs.acs.org/doi/abs/10.1021/ct800573m <http://pubs.acs.org/doi/abs/10.1021/ct800573m>

It is also described in the manual (see the descriptions for “ntt=3” and “ig”).

HTH,
Jason

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 29 2015 - 07:00:04 PDT
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