You don't "turn on" those modifiers, you choose to shift the potential. (In the future there might be more options.) Shifting the potential is quite different from the action of vdwtype=shift, see manual 4.1, 7.3. The potential should be the integral of the force, if you want it to mean anything. Whether that's important depends what you're doing and want to observe. The potential is irrelevant if you are just sampling space to see what is there, but it's critical if you're trying to compute thermodynamic properties.
Mark On Thu, May 23, 2013 at 10:46 PM, Bin Liu <[email protected]> wrote: > Dear Mark, > > Could you elaborate on your answer? In my group cutoff scheme, I used > > ns_type = grid ; search neighboring grid cels > nstlist = 5 ; 10 fs > rlist = 1.3 ; short-range neighborlist cutoff (in nm) > rcoulomb = 1.3 ; short-range electrostatic cutoff (in nm) > rvdw = 1.0 ; short-range van der Waals cutoff (in nm) > vdwtype = Shift > rvdw_switch = 0.9 > > What is the advantage of turning on coulomb-modifier and vdw-modifier in > terms of physical or chemical accuracy of simulations? Thanks. > > Bin > > > > Those modifiers shift only the potential, as manual 7.3 points out. So the > forces and sampling are unaffected, so it does not surprise me that APL is > unaffected by the use of such a shift. If your group cutoff scheme was > unbuffered (rlist <= max(rcoulcomb,rvdw) and nstlist > 1), then if the > observed difference is significant, then that could be the reason. > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
