From: Peter Freddolino (petefred_at_umich.edu)
Date: Fri Jun 09 2017 - 10:10:21 CDT
Following up on that, it would be helpful to know what type of CG model
you're using and what your other parameters look like...
On 06/09/2017 10:45 AM, Richard Overstreet wrote:
> 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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