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? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- 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.
