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

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Sat Jun 20 2009 - 12:46:25 CDT

You can always physically move one molecule by making an atomselection
and then translating the selection along the various axes (i.e.
"translate x by A angstroms").

Also, may I ask why you are solvating in a water sphere? With current
computational capacity, a water box is recommended for optimal
arrangement of periodic boundary conditions.

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu

On Jun 20, 2009, at 11:02 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
>

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