Re: VMD/NAMD two identical molecules solvate in a water sphere

From: Joshua Adelman (
Date: Sat Jun 20 2009 - 12:21:49 CDT

Hi David,

If both molecules have identical coordinates, then VMD won't separate
them automatically. You can translate one of the molecules a
particular distance using the TCL command line. See:

While it is standard practice to solvate with a shape that you can
apply periodic boundary conditions to, I imagine that you could use
the solvate plugin and a little tcl scripting to create a sphere. What
you'd want to do is to create a box around your protein that is more
than generous in size, such that it could contain the sphere that you
want. Then you could select atoms that are within some distance (the
radius of your sphere) from the center of the box (or an atom that is
approximately at the center), and write a new PDB just with those
atoms. Alternatively you could use the script supplied with the NAMD

Best of luck.


On Jun 20, 2009, at 9:02 AM, David Jiang wrote:

> Hi all,
> My name is David and I am a high school student interning at the
> University of Houston. I'm trying to solvate two identical molecules
> in a water sphere but I have been unsuccessful for a number of
> reasons. I do not know how to make it so that VMD doesn't overlap
> the two identical molecules and instead, allows both molecules to be
> seen. In addition, is there a way to solvate this two molecule
> structure in a water sphere using NAMD? I would really appreciate
> any help and thank you all for your time.
> David

Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley
Berkeley, CA 94720 USA

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