[gmx-users] Neutralizing

mohammad r mohammad.r0325 at yahoo.com
Thu Mar 10 08:42:56 CET 2016

Thank you Justin for your help. 

    On Wednesday, March 9, 2016 6:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:


On 3/9/16 1:42 AM, mohammad r wrote:
> Thank you Parham and Justin, Excuse me I have another question, in simulation
> of a water-peptide system, is it necessary to use QM/MM simulation during the
> entire process? Because I didn't see it in the tutorials. By the way I
> generated the pdb file by using charmm-gui then import it in amber to get the
> topology and coordinate files, finally I converted the topology and
> coordinate files to gromacs format and did the rest of simulation by gromacs.
> but I didn't run QM/MM simulation. Does it make trouble in the results?

The technique(s) used depend on the scientific question(s) being posed before 
doing the simulations.  If you expect some reactions, etc. to be taking place, 
then you need QM/MM.  If you just want to simulate a peptide over time, then 
plain MD is fine.  Methodological details like this should be decided long 
before one approaches a keyboard :)



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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