Hi,
On Mon, Jan 10, 2011 at 11:19 PM, Shesh Nath <sheshnath65.gmail.com> wrote:
>
> but when temperature arrise to 250K ,one strand of DNA is disappeared.
> I want to my heating step is right or wrong.
> Give me suggestions
First, you will have to clarify what you mean by 1 strand having
'disappeared'. How have you determined this (coordinate analysis,
visualization etc)?
Second, whether you are right or wrong largely depends on what you are
hoping to achieve with this simulation. If your overall goal is to
perform simulations of DNA at close to biological conditions you are
certainly not going to get there with an in-vacuo (ntb=0, igb=0)
simulation. I would suggest you check out the Amber tutorials,
particularly
http://ambermd.org/tutorials/basic/tutorial1/ which
actually will take you through simulation of a nucleic acid in various
conditions.
-Dan
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> --
> SHESH NATH
> RESEARCH SCHOLAR,
> THEORETICAL CONDENSED MATTER PHYSICS,
> DEPARTMENT OF PHYSICS,
> BANARAS HINDU UNIVERSITY,
> VARANASI-221005
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Received on Tue Jan 11 2011 - 07:30:05 PST
