Re: cgmd stability

From: wang (c00jsw00_at_nchc.org.tw)
Date: Wed Feb 25 2009 - 21:43:41 CST

Dear Peter ,
Thanks for your help. I have overcome the problem . By the way, the
new martine CG FF has been released.
Would you plane to transform the new martine CG FF to the charmm format ?
And Could you tell me how to transform the new martine CG FF to the
charmm format ?
Thanks a lot

Y.T Wang

Peter Freddolino 提到:
> 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
>>>
>>>
>>>
>>>
>>>
>
>
>
>
>


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:21:45 CST