[gmx-users] Regarding structure conformation

Vytautas Rakeviius vytautas1987 at yahoo.com
Mon Apr 3 08:33:11 CEST 2017

MD can not simulate chemical reactions. What you can do prepare different forms with acpype and compare all in some way.

    On Monday, April 3, 2017 6:51 AM, Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:


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
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
With Best Regards,

Ph.D Student

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