Re: DNA Simulation

From: Michael Cooney <>
Date: Mon 8 Jan 2001 14:57:31 -0500 (EST)

Hi, Troy,

I had nearly the same thing happen to me, except that the strands did
_not_ remain together--they translated apart (but did not rotate relative
to each other). Right now I am trying belly dynamics to constrain the
terminal base pairs on the DNA duplex. My system consisted of a DNA duplex
complexed to a 60-aa peptide, which might account for the protein
remaining bound to one DNA strand while the other strand floats away.
If you would like a sample belly dynamics input I will be glad to e-mail
one to you. If the only problem is migration outside the water box, then
this may be an imaging issue, and the ptraj program may help.
Good luck!

Best regards,

Michael Cooney
Dept. of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602

On Mon, 8 Jan 2001, Troy Bothwell wrote:

> During a 2ns simulation of a 14-mer dna duplx, part of the solute "floated"
> outside the periodic box of water. The strands remained together. Does
> anyone know what causes this? The boundaries are 10 angstroms away from the
> duplex on all sides initially.
> Thanks for any input,
> Troy Bothwell
> Graduate Student
> University of Nebraska Lincoln
Received on Mon Jan 08 2001 - 11:57:31 PST
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