[gmx-users] The small organic molecule occurred deformation during simulation

[Justin Lemkul]

On 8/5/17 2:59 PM, yujie liu wrote:
> 
> Mr Justin:
> 
> I have tried to do energy minimization in this situation which only existing small molecule in water, I found  the structure of organic molecule didn’t become distortions. I think  the distortions of organic molecules are due to these stronger interactions between small molecules and enzyme, because there is a enzyme molecule in the previous simulation. Do you think this consideration is correct? In the case, do you think this phenomenon  is normal? What’s more, I checked out the top file of small molecules and don’t find error and include the information of improper dihedrals.
> 

Or your energy minimization simply indicates a strained initial structure that 
isn't fully relaxed.  Real MD sampling is important here; energy minimization 
won't tell the whole story, at least not in any reliable way.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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