[gmx-users] Why not PBC for implicit solvent?
jalemkul at vt.edu
Tue Feb 26 12:56:40 CET 2013
On 2/25/13 10:30 PM, Yun Shi wrote:
> Hi everyone,
> Previous posts mentioned setting pbc = none for MD simulations with
> implicit solvent. But I am trying to see the behavior of certain
> concentration of ligands (small molecules, no big biomolecules) in
> solvent, so I wonder if setting pbc = xyz would cause any problem for
> my system?
I see no theoretical problem with running NVT with "pbc = xyz" with implicit
solvent, but definitely not NPT since the box will shrink inwards and lead to
periodicity artifacts (if it even remains stable at all). I usually set a
nonperiodic box because it allows me to use the infinite cutoff approach, which
is the only one I have found to give sensible results.
> Should I also stay with the normal cutoff values for vdw and coul interactions?
Maybe, but do some serious testing before relying on the results. Maybe for
small molecules a finite cutoff will work, but for proteins I have tried cutoffs
of 1.0, 2.0, 4.0, and even 8.0 nm and all have unfolded or distorted.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users