Re: How can I move an atom by 10nm with a step of 0.1nm

From: Brian Bennion (
Date: Tue Oct 05 2004 - 10:44:01 CDT

Hello Shahid,

This may sound a bit complex, but you could take advantage of the
vmd/namd interactive dynamics feature. A short script in vmd will allow
you to move the atoms precisely and the autoimd extension would allow for
minimization of the system with fixed and free atoms.

Just my $0.02 worth


On Mon, 4 Oct 2004, Shahid Qamar wrote:

> Hi,
> Situation: Lignad-Receptor Molecule
> Ligand has an atom O
> Receptor has an atom C
> O is fixed and want to move C by 0.1nm and then keep its positon fix and
> then minimize the system
> Then move C by 0.1 step and keep the distance between O and C fixed and
> minimize the system
> Then keep going till a desired separation between C and O is attained.
> Question: Is there any way that I can write tcl script that can move the C
> by 0.1 nm and then keep the distance fix?
> I know i can move any atom by mouse but that could give me more or less than
> 0.1 separation.
> Any idea???
> Thanks in advance for the help
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**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **

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