Hi Justin, Will appreciate any suggestions about the error am getting with distance_restraints. Thanks.
regards, Dave On Thu, Oct 31, 2019 at 1:39 AM Dave M <dave.gro...@gmail.com> wrote: > Hi Justin, > > Thanks, not sure [distance_restraints] also does not work for me. Though > pull code works (like shared by other user Mustafa in recent discussions). > > My top files contain this: > [ intermolecular_interactions ] > > > [ distance_restraints ] > > ; ai aj type index type’ low up1 up2 fac > > 1 155 1 0 1 0.0 0.3 0.4 1.0 > > > I get this error: > > NMR distance restraints with multiple copies of the same molecule are > > currently only supported with ensemble averaging. If you just want to > restrain > > distances between atom pairs using a flat-bottomed potential, use a > restraint > > potential (bonds type 10) instead. > > I do not have multiple copies of the same molecule (except water > molecules!) and the atom numbers here belong to two different molecules. I > also tried using type' = 2 but still error remains the same. Would have > been great if distance_restraints work as it seems to be bit cleaner way > than modifying a pull code. I want to keep number of small molecules near > to a rod like bigger molecule; just like beads on a string. So > distance_restraints or something similar will be great. > > Dave > > On Tue, Oct 29, 2019 at 5:45 AM Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 10/28/19 6:21 PM, Dave M wrote: >> > Hi Justin, >> > >> > Thanks for your reply but am getting error suggesting a intermolecular >> > chemical bond is not allowed: >> > >> > Program: gmx grompp, version 2016.4 >> > >> > Source file: src/gromacs/gmxpreprocess/convparm.cpp (line 649) >> > >> > Fatal error: >> > >> > The intermolecular_interaction can not contain chemically bonding >> > interactions >> > >> > [ molecules ] >> > >> > ; name number >> > >> > molA 1 >> > >> > molB 1 >> > >> > W 2420 >> > >> > >> > [intermolecular_interactions] >> > >> > [ bonds ] >> > >> > 1 158 1 0.4 2000 >> > >> > This is coarse-grained model and as a simple test I used global atom >> > numbers between two water single particles (intermolecular) but I get >> the >> > same error. >> >> In that case, use a [distance_restraints] directive under >> [intermolecular_interactions] (though this will limit your domain >> decomposition setup) or use the pull code to maintain a restraint rather >> than messing with the topology. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalem...@vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> 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.