[gmx-users] Exploding poly-serine

[Warren Gallin]

David,

	That is probably it, I had a 2-femtosecond step and no bond  
constraints.  Obviously I need to read up on the pros and cons of the  
various restraint regimes.

	I guess that would be consistent with the sudden explosion after  
along period of stable running.

	Why poly-Ser would be more susceptible to this than poly-Pro, poly- 
Asp or poly-Gly is not obvious to me, but I am sure that there is a  
reason out there somewhere.

Thanks,

Warren Gallin

On 26-Aug-09, at 10:48 AM, David van der Spoel wrote:

[Details deleted]

>>
>>   So my questions are:
>>    1) Am I missing some obvious step in setting up a stable  
>> simulation?
>>    2) Is it true that the high internal force present at the end of  
>> the initial energy minimization could be the root of the problem?
>>    3) If so, is there an obvious method for relaxing the system  
>> into a more stable state prior to the main MD run?
>
> What time step are you using? Since you are not using bond- 
> constraints the time step should be on the order of 0.5 fs.
>
>> Warren Gallin
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>
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala  
> University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
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