AMBER Archive (2007)

Subject: Re: AMBER: Help: 1 ns for implicit solvent (GB) calculations, enough?

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Feb 14 2007 - 06:26:31 CST

1ns is not enough unless the system does not change much or is
very small. how much is "enough" depends on the goal of your simulations.
looking at fluctuations in structure of a large protein is different from
trying to predict structure for a peptide.

On 2/13/07, Catein Catherine <askamber23_at_hotmail.com> wrote:
>
> Dear Sir/Madam,
>
> I read from the literature that implicit solvent models convergent faster,
> just it may reach equilbrium faster than explicit solvent. Thus, I am
> writing to ask what is the typical stimulation time for a system with 700
> residues using implicit solvent (GB) in Amber?
>
> I noted that the potential energy remain more or less constant after 200
> ps,
> then, I run the production period for a further 1 ns. Is it an acceptable
> time for implicit solvent (GB) calculations? if not, how long should be
> used
> for publication purposes?
>
> Best regards,
>
> Catherine.
>
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
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Stony Brook University        E-mail: carlos.simmerling_at_gmail.com
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