On 12/13/17 12:24 PM, Shi Li wrote:
------------------------------ Message: 6 Date: Wed, 13 Dec 2017 11:41:26 -0500 From: MD <refm...@gmail.com> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] my minimization structure looks like a messy box? Message-ID: <cappxtgrhhwov-+nebc2m4_njsjcmwho37hmffz3tbqe7pak...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" It looks like this https://drive.google.com/open?id=1DMy1otIYQZD8uxF6sZaZzZK4qN1z_qyD On Wed, Dec 13, 2017 at 11:04 AM, Justin Lemkul <jalem...@vt.edu> wrote:If you are talking about all the lines, try using “-pbc mol" in the trjconv, this should get rid of all of them. But I haven’t have that after em.mdp. Did you generate velocity in energy minimization?
There can be no velocities during energy minimization. The snapshot provided just suggests a solute that was not centered in the box prior to carrying out EM, hence it is "broken" across boundaries.
-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.
