all-bonds and none work, so I assume, as alternating between these settings speeds up the EM. However, I always see the protein move around in the box after centering, so just re-center after reaching pressure and temp stability before the extended pre-run equilibration with set restraints (which seems to keep the protein where I want at this point).
Sincerely,
Stephan Watkins
Gesendet: Sonntag, 03. November 2013 um 05:38 Uhr
Von: "Gianluca Interlandi" <gianl...@u.washington.edu>
An: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Betreff: [gmx-users] DPOSRES and energy minimization
Von: "Gianluca Interlandi" <gianl...@u.washington.edu>
An: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Betreff: [gmx-users] DPOSRES and energy minimization
Is it possible to use position restraints: define = -DPOSRES during an energy minimization? I tried to do that but it looks like all atoms are moved during minimization: ; VARIOUS PREPROCESSING OPTIONS = title = cpp = /lib/cpp include = define = -DPOSRES ; IMPLICIT SOLVENT OPTIONS = implicit-solvent = GBSA gb-algorithm = OBC ; RUN CONTROL PARAMETERS = integrator = steep ; start time and timestep in ps = tinit = 0 dt = 0.001 nsteps = 1000 ; ENERGY MINIMIZATION OPTIONS = emtol = 0.00001 emstep = 0.01 nstcgsteep = 1000 Thanks! Gianluca ----------------------------------------------------- Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. ----------------------------------------------------- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
