Re: cgmd stability

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Feb 26 2009 - 02:13:16 CST

Hi,

a couple grad students in the group here are doing this conversion,
although it has turned out to be more complicated than one would expect.
 This has been discussed previously on namd-l; there should be an
announcement when it is finished.

Best,
peter

wang wrote:
> 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
>>>>
>>>>
>>>>
>>>>
>>>>
>>
>>
>>
>>
>>
>

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