On Wed, 2014-04-09 at 13:13 -0400, Christopher A Thiebaut wrote:
> There is no way to control for this when you solvate the box. After
> you solvate the box, you must do a short NVT simulation to allow the
> solvent to distribute evenly into any such gaps.
I agree with most of this, but just warn that you should run just enough
NVT dynamics to 'heat' the system up to a reasonable temperature (which
just avoids potentially strange artifacts from launching NPT simulations
starting from 0K structures). My protocol involves no more than maybe
100-200 ps of 'slow' heating followed by NPT to stabilize the density.
If the box is too big, you will form bubbles that will be hard to press
out following NVT dynamics that are too long (after all, water boils at
low temperatures under conditions of low pressure, and the water models
correctly demonstrate this behavior).
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 09 2014 - 10:30:06 PDT
