[gmx-users] trajectory analysis

[Justin Lemkul]

On 12/15/16 11:05 AM, maria khan wrote:
> Dear gromacs users..
> I have the following questions.
> 1) ::how i analyse trajectory using VMD?
>

Consult the VMD documentation, tutorials, and mailing list.

> 2)::Trajectory analysis for overall protein structure stability??
>

Define "overall protein structure stability."  This can mean a lot of different 
things.

> 3)::protein - ligand interaction i-e H-bonds and anyother interactions.??
>

gmx hbond calculates hydrogen bonds.  Other analysis tools are listed in the 
online manual.

> 4)::trajectory analysis for free energy binding of protein and ligand??
>

This is not a mere task of analysis.  You'll need to do a proper set of free 
energy calculations.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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