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.
-Justin
On Monday, April 3, 2017 6:51 AM, Dilip H N <cy16f01.di...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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