[gmx-users] Why not PBC for implicit solvent?

Justin Lemkul 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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