[gmx-users] Regarding structure conformation

Justin Lemkul jalemkul at vt.edu
Mon Apr 3 13:51:41 CEST 2017

On 4/3/17 2:23 AM, Vytautas Rakeviius wrote:
> MD can not simulate chemical reactions. What you can do prepare different forms with acpype and compare all in some way.

External tools aren't even necessary.  One just needs to select the proper 
termini with pdb2gmx.


>     On Monday, April 3, 2017 6:51 AM, Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:
>  Hello,
> I have a non zwitterionic glycine molecule, and have solvated it with
> water, created topology and ran the simulation...and during EM, NVT, MD
> runs the non zwitterionic form of glycine is still as it is, it hasn't got
> converted into zwitterionic form (which is the most stable form of glycine
> in water/solvent)...
> So how can i convert non zwitterionic glycine form to its zwitterionic
> form..??
> Ideally it should get converted into its most stable form during solvation,
> but why is it not getting converted..?? how can i solve this issue..?? Is
> there anything wrong.??
> Thank you


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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