Re: cgmd stability

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Feb 24 2009 - 04:22:31 CST

You need to use 1-2 exclusions, not scaled1-4 exclusions, for CG
simulations. You should double check your other parameters to make sure
that they match up with those from the rbcg papers...
Best,
Peter

wang wrote:
> Dear Peter ,
> I tried the time step (5 fs , 4 fs .....1 fs) and the error message
> still appeared .
> --------------------------------------------------------------------------------------
> ENERGY: 2000 1007.9480 994.1360 2070.1208 0.0000
> 0.0000 15480610.9536 0.0000 0.0000 23430.1580
> 15508113.3163 311.0564 15588509.6282 15287023.4586 311.0564
> 1761774.9487 1761774.9487 2744000.0000 1761774.9487 1761774.9487
>
> ERROR: Atom 18483 velocity is 594097 1.44783e+06 2.65815e+06 (limit is 5000)
> ERROR: Atom 18529 velocity is -593137 -1.44994e+06 -2.65792e+06 (limit
> is 5000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> FATAL ERROR: Bad global exclusion count!
>
> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
> --------------------------------------------------------------------------------------------
>
> Y.T Wang
>
> Peter Freddolino 提到:
>> Please don't send such large attachments to an entire email list, and
>> certainly not as plain text.
>>
>> For your problem, what timestep and exclude settings are you using?
>>
>> Peter
>>
>>
>>
>>
>

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