Re: control distance between solvent and solute

From: Jim Phillips (
Date: Wed Jul 20 2011 - 11:57:16 CDT

The VMD solvate plugin has options for both of these for a water box:

vmd > solvate
Info) Usage: solvate <psffile> <pdbfile> <option1?> <option2?>...
Info) Usage: solvate <option1?> <option2?>... to just create a water box
Info) Options:
Info) -o <output prefix> (data will be written to output.psf/output.pdb)
Info) -s <segid prefix> (should be either one or two letters; default WT)
Info) -b <boundary> (minimum distance between water and solute, default 2.4)

The Tcl solvate interface also has a Boundary field and a Waterbox Only

The tutorials are only an introduction to the tools so they do not cover
all of the available options. Whatever the tutorial does to remove waters
near the protein from the sphere should also have a "within X of"
selection that can be modified to change the distance or removed to
produce only a sphere of water.


On Sat, 16 Jul 2011, Kang Hee Cho wrote:

> Dear NAMD users,
> I solvate the protein in water sphere(TIP3 water model).
> Can I control distance between solvent and solute?
> I can't find the option in NAMD tutorial.
> Another question is how to only load water molecule.
> Any suggestions will be appreciated.
> Thank in advance, Kang Hee.

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