Re: membrane simulation Constraint failure in RATTLE algorithm

From: snoze pa (snoze.pa_at_gmail.com)
Date: Thu Feb 17 2011 - 10:00:44 CST

Hi Jeff,
 Thank you very much for your time and suggestions. The time step of 1 fs
working fine.. even with 5000 step of minimization. I already crossed 200ps
and no problem at all.
Regards
S

On Wed, Feb 16, 2011 at 10:18 PM, Jeffrey Potoff <
jpotoff_at_chem1.eng.wayne.edu> wrote:

> Yes, the bilayers were electrically neutral at all times. You can start
> with just the bilayers in water. Once you get a stable system you can
> remove some of the water and replace with the ions of your choice.
> Sometimes with these kinds of simulations you need to run1000-100000 steps
> with a very small time step (<0.5 fs) to get rid of all the rattle errors.
>
> Regards,
> Jeff
>
>
>

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