[gmx-users] radius of gyration in REMD of protein
jalemkul at vt.edu
Fri Aug 19 13:47:32 CEST 2016
On 8/18/16 10:28 PM, YanhuaOuyang wrote:
> Hi, I am running a REMD of a protein, which ranged from 270 to 500K in
> explicit water model with 60 replicas, and I stop to analyse the REMD data
> after running for 50ns. I use the demux.pl script to get the continue the
> coordinate for each replica. Then I calculate the Rg value for each replica.
> However, the Rg fluctuation of each replica differs dramatically, some
> fluctuate dramatically, some converge well. Do someone knows the reason, or
> the fluctuation is normal ? How can I check my REMD is running correctlly?
Suddenly switching to a high temperature can (and usually does) induce large
structural changes, hence the point of REMD. This is why people most often
(nearly always) focus on structure properties of the ensemble-continuous ground
state. Behavior at high temperature is usually very artificial and you usually
care most that you are getting sufficient exchanges to cross barriers so that
the ground-state sampling is enhanced.
It could also very well be that you have some disordered loops/termini that
simply go a bit crazy at high temperature, which is not likely very relevant to
the actual dynamics. Watching the demuxed trajectory(ies) that are showing
large Rg variation should point out the exact behavior. Step 1 is always to
watch the trajectory!
> the commad of Rg calculation is below: gmx gyrate -s md_0_0.tpr -f
> *_continue_trajectory_pbc_mol.xtc -o gyrate_*.xvg
> Best regards, Ouyang
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
More information about the gromacs.org_gmx-users