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

Justin Lemkul 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.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list