Great, thanks. I believe this necessitates an acknowledgment. You go by J. A. Lemkul in your papers, correct?
On Mon, Mar 12, 2018 at 4:56 PM, Justin Lemkul <jalem...@vt.edu> wrote: > r > > On 3/12/18 6:54 PM, Alex wrote: > >> Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point, it's >> still a small system. My sampling pull code is below, I only modified the >> bare minimum to work with the new pull code syntax and to enable spherical >> slices (radius varying from near-zero to 1.5 nm): >> >> pull = yes >> pull-coord1-type = umbrella >> pull_ngroups = 2 >> pull_ncoords = 1 >> pull_group1_name = CL >> pull_group2_name = CNT >> pull_coord1_geometry = distance >> pull_coord1_groups = 1 2 >> pull_dim = Y Y Y >> pull_coord1_rate = 0.0 >> pull_coord1_k = 1000 >> pull_start = yes >> >> CNT is the colloquial name for our membrane. I'm trying to be >> extra-careful >> this time, so I will really appreciate if you see anything else that looks >> wrong. Another quick question: it is my understanding that the value of k >> will control the histogram width. Is 1000 a reasonable choice overall? >> > > No way to know. It depends on the window spacing and the forces acting in > the system. I don't know that anyone has come up with a way to actually > know what's "right" for umbrella sampling other than empirical assignment. > > Everything else looks reasonable to me. > > > -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.
