On 3/15/17 6:19 AM, stellatof wrote:
Dear all,
I have a question regarding the use of "POSRES" in .
In the umbrella sampling tutorial it says that POSRES is used to keep one chain
as an immobile reference in the pulling procedure. What is the effect of POSRES?
Does it keep the molecule center of mass fix or does it restrain the positions
of atoms inside the molecules? According to the manual I tought the latter one,
but then I don't understand how this helps in having an immobile reference.
By applying a harmonic biasing potential to each non-hydrogen atom with an
origin for that potential at the starting coordinates, the motion of each heavy
atom is restricted.
What problem would one have if not using the POSRES?
In the tutorial's case, the strength of the many hydrogen bonds between the
peptide chains would simply causing the entire assembly to be dragged across the
simulation box rather than inducing dissociation of one peptide. Larger biasing
forces lead to distortion of the structure. The use of restraints in the
tutorial (and corresponding paper, please read it as technical aspects are
explained in more detail with references to other amyloid papers that use
similar approaches) is not necessarily applicable to other umbrella sampling
studies.
In the simulations I performed, when I pull one molecule, the one I restrained
using POSRES keeps its center of mass stable and has only small changes in its
internal structure. Is it the expected behaviour?
Yes, but whether or not you need restraints is the larger question. For
instance, I see no reason to use the tutorial's approach for a protein-ligand
complex, in which the interactions will be comparatively weak (and also require
a different pull vector setup, anyway).
-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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