[gmx-users] RMSD analysis

[Justin Lemkul]

On 6/6/17 2:12 AM, RAHUL SURESH wrote:
> Dear Users
> 
> *Exp procedure:*
> I have simulated the protein monomer for 150ns. Using the 150ns conformer,
> ligand is docked to the protein using autodock and the simulation is
> carried out for 50ns.
> 
> *Analysis:*
> 
> Is it possible to compare my RMSD, RMSF, ROG analysis of complex system
> with that of monomer? If yes which part of the monomer trajectory should be
> considered.?
> 

This is up to you to determine in light of whatever your goals are in running 
the simulation.  What are you trying to test or determine?  Unless the protein's 
stability is seriously impacted by the ligand, RMSD and Rg are useless.  RMSF 
might be useful if there are motions that are amplified or damped by ligand 
binding.  Run the analysis and see what happens on a per-residue basis.

-Justin

-- 
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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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