On 10/5/16 5:24 PM, Alexander Alexander wrote:
Dear gromacs user, I was wondering how long normally should be the pulling time in one step before the final umbrella sampling? For instance in the Aβ42 protofibril umbrella sampling used in tutorial, the applied simulation times are as following referring to the original paper: Production Normal MD: 100 ns Pulling time : 500 ps MD in each windows : 10 ns
These are like any other simulation. They need to be sufficiently long to converge the properties of interest.
The second question is that can we limit the pulling region to pull away for example A from B as 3 nm in the pulling run(not in the final umbrella sampling)?
The length of the reaction coordinate should be sufficient to obtain "non-interacting" species to fully describe the binding free energy. Of course, such states are not generally possible in MD with PME since there are always long-range forces, but if the molecules are sufficiently beyond the short-range cutoffs, it's usually good enough.
-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.
