[gmx-users] The small organic molecule occurred deformation during simulation
jalemkul at vt.edu
Mon Aug 7 16:31:40 CEST 2017
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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