[gmx-users] Protein+ligand complex

Justin Lemkul jalemkul at vt.edu
Fri May 15 13:58:16 CEST 2015

On 5/15/15 1:36 AM, Kashif wrote:
> I have done MD simulation of my protein and ligand docked complex. My
> protein is having 900 amino acids. When I use g_rms to analyse rmsd, the
> graph is too short. Currently I am simulating my protein for 5 ns. Should I
> increase my ns for such big protein and ligand complex?

5 ns of dynamics on a protein generally tells you nothing of any reliability.


> On Tue, May 12, 2015 at 4:41 AM, Kashif <kashifzamir180.mk at gmail.com> wrote:
>> Greetings of the day,
>> Can I use nvt.mdp and npt.mdp parameter file given in tutorial (
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html)
>>   for my 5 ns production run? As the tutorial shows 100 ps nvt and npt
>> equilibration and 1000 ps (1 ns) MD Simulation run. Which parameter should
>> be changed if there is any problem.
>> What are the post-simulation analysis commands used for the analysis for
>> protein+drug complex?
>> regards
>> Kashif


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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