Hi, There have been some improvements to the pull code, but I don't know offhand whether they apply here. Do consult the 2019 release notes for clues.
Mark On Sat., 23 Feb. 2019, 06:11 Ayesha Fatima, <ayeshafatima...@gmail.com> wrote: > Dear All, > I am using Gromax 2019 and running an umbrella sampling for two proteins. > It is a simple pulling simulation. It is giving me the following error > > > ERROR 1 [file md_pull.mdp]: > When the maximum distance from a pull group reference atom to other atoms > in the group is larger than 0.5 times half the box size a centrally > placed atom should be chosen as pbcatom. Pull group 1 is larger than that > and does not have a specific atom selected as reference atom. > > > ERROR 2 [file md_pull.mdp]: > When the maximum distance from a pull group reference atom to other atoms > in the group is larger than 0.5 times half the box size a centrally > placed atom should be chosen as pbcatom. Pull group 2 is larger than that > and does not have a specific atom selected as reference atom. > > Pull group natoms pbc atom distance at start reference at t=0 > 1 9157 4579 > 2 589 5113 0.300 nm 0.300 nm > Estimate for the relative computational load of the PME mesh part: 0.14 > > > ---------------------------------------------------------------------------------- > Is there anything to be added in the pull code? > > Thank you > Regards > -- > 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.
