[gmx-users] From: Graduate Student protein active site inquiry

Justin Lemkul jalemkul at vt.edu
Sun May 7 20:03:46 CEST 2017

On 5/5/17 7:23 PM, Felix Y Yang wrote:
> Thanks for the reply.
> I'm trying to test out a theory that enzymes gain "heat" from their
> substrate after the catalytic reaction finishes, thus my plan to heat up
> the active site. Is there a better approach to testing this theory?

The challenge you're going to face is if you assign different parts of the 
protein to different thermostat groups (tc-grps) then you're going to have a 
defined interface that are held at different temperatures.  The thermostats will 
withdraw or supply heat to maintain the target temperatures, so it's not clear 
to me how you'll address the problem at hand.  Maybe you can equilibrate with 
separate groups (e.g. NVT) and then continue with NVE to see how the energy 
flows between the groups, but this will likely happen extremely fast so you'll 
have to save velocities pretty frequently.

> How would I specify the groups?

Use make_ndx to create groups and supply that file to grompp -n.



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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