On 9/18/16 11:35 PM, Yoo Chan Myung wrote:
Dear gmx users,

I'm trying to simulate membrane penetration with peptide(octamer) using
GROMACS-5.1.2. and I referred the Umbrella Sampling tutorial by Dr. Justin
Lemkul.

After 100 ps umbrella_NPT run, peptides confirmations are still kept in
their initial coordinates. However, after 10ns of umbrella_MD, I cannot get
reliable results for WHAM analysis because the confirmations are quite
deviated from the umbrella_NPT structures.
(plz, refer two results,
https://www.dropbox.com/s/maqwjww8nozmcn6/q_a.jpg?dl=0)

So, my question is should I have to use position restraint for moving
ligands? or just extend simulation time for umbrella_NPT to get equilibrium
structures for umbrella_MD?


What would you restrain? Don't fall into the trap that many people seem to do (despite me warning against it...) and try to follow the tutorial too literally. Restraining the peptide in the tutorial had a specific purpose. it's something that probably 99% of umbrella sampling simulations should NOT use.

Your structure is basically just falling apart. You may need some inter-peptide restraints to preserve the geometry, but then deconvoluting all of that into a meaningful PMF for just pulling the aggregate through the membrane becomes very challenging.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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