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

[Justin Lemkul]

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

-- 
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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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