Sorry, i can't understand, what do you mean"-zprof0" option? Could you please give me an example?
On 3 Mar 2018 16:47, "Justin Lemkul" <jalem...@vt.edu> wrote: On 3/3/18 7:02 AM, rose rahmani wrote: > Hi > > I use umbrella sampling to calculate PMF, for studying the interaction of > different aminoacids with nanosheet separately. But at the minimum distance > from sheet, potential is zero for all PMF diagrams. I mean there isn't any > positive potential even at closest distance of aminoacid from sheet. I did > pulling and sampling manyyy times with different rates ...,still the same > problem... how could it be possible?What is the problem? I really get > confused. There isn't any closer distance to sample it. > Would you please help me? > WHAM works by assigning the leftmost (lowest index) window a free energy value of zero, and then constructs the rest of the profile relative to it. You can adjust this with the -zprof0 option. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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. -- 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.