On 10/26/14 3:43 PM, Agnivo Gosai wrote:
Dear Users I have gone through the tutorial on umbrella sampling by Dr. Lemkul and am using the methodology described therein for running my own simulations. It is explained that :- "GROMACS calculates distances while simultaneously taking periodicity into account. This, if you have a 10-nm box, and you pull over a distance greater than 5.0 nm, the periodic distance becomes the reference distance for the pulling, and this distance is actually less than 5.0 nm! This fact will significantly affect results, since the distance you *think* you are pulling is not what is *actually* calculated." Are there any guidelines for assigning the COM position of my biomolecule complex and the x,y,z dimensions of my simulation box keeping in mind the above explanation. Or I should go about it in a trial and error basis?
Trial and error is an awfully expensive way to determine what you need to do, when it's rather straightforward to figure out. Determine the length of the reaction coordinate you need. Based on the length of that vector in the dimensions along which the pulling takes place, it is simple to figure out the minimum size of the box in each dimension. If using pressure coupling, add a small buffer to the size to account for fluctuations.
-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.
