Re: solvent other than water

From: Jeff Comer (
Date: Wed Jan 06 2016 - 13:39:14 CST


I use CGenFF to parameterize the solvent molecules and then assemble
the systems using PackMol:

As PackMol only eliminates steric clashes, you need to run for some
time to equilibrate the solvent.

Another option would be to equilibrate a box of solvent and then use
the VMD Solvate plugin. Here's an example of using Solvate with a box
of coarse grained Martini water (defined by "martini_water.psf" and

solvate sys.psf sys.pdb -b 4.7 -spsf martini_water.psf -spdb
martini_water.pdb -stop -ws 36.4428 -s W -ks "name
W" -minmax {{-100 -100 -250} {100 100 250}} -o sys_sol


Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Wed, Jan 6, 2016 at 12:17 PM, Deng, Jinxia (Nancy)
<> wrote:
> Happy New Year to all!
> Just wonder how or where to access solvate models other than water...
> Only hint I have is through as listed in a membrane protein tutotial by NAMD, but the link is not working any more.
> Looking forward to any of your advice.
> Thanks,
> Nancy

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