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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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