Re: coarse-grained simulations with errors "Atoms moving too fast" and "low global exclusion"

From: Richard Overstreet (roverst_at_g.clemson.edu)
Date: Fri Jun 09 2017 - 09:45:06 CDT

See here:

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2015-2016/2439.html

and

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2015-2016/2431.html

In brief the time step will affect the accuracy of your integrator and
you are limited in the choice by the fastest degree of freedom in your
simulation.

On 06/09/2017 09:39 AM, Yaxin An wrote:
> Hi
>
> I am running coarse-grained simulations with a time step of 5fs. When
> the system sizes increased from 100 molecules to 500 or 1000
> molecules, the simulations crushed after running for hundreds of
> steps. The errors are "atoms moving too fast" or "low global
> exclusion". When I used a timestep of 10fs, these errors emerged after
> running for hundreds or about one thousand steps.
>
> I have to restart the simulations, but after some time they crushed again.
>
> Is there someone who knows how to fix this problem?
>
> Thanks
>
> Bests;
> Yaxin

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