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 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
