It can be. Lack of explicit degrees of freedom of solvent can make achieving equipartition tricky. With CHARMM27 and virtual sites in implicit solvent, I have sometimes found it necessary to use a sub-femtosecond time step at the start of equilibration, even where there were no atomic clashes. Maybe the system was just unlucky with generating velocities, though :-)
Mark On Aug 28, 2013 7:16 AM, "Gianluca Interlandi" <gianl...@u.washington.edu> wrote: > How important is it to do gentle heating (using simulated annealing) with > GBSA? Often with explicit water it is enough to perform some equilibration > with positional restraints. Would it be enough to do the same with implicit > solvent? > > Thanks, > > Gianluca > > ------------------------------**----------------------- > Gianluca Interlandi, PhD gianl...@u.washington.edu > +1 (206) 685 4435 > > http://artemide.bioeng.**washington.edu/<http://artemide.bioeng.washington.edu/> > > Research Scientist at the Department of Bioengineering > at the University of Washington, Seattle WA U.S.A. > http://healthynaturalbaby.org > ------------------------------**----------------------- > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
