AMBER Archive (2007)

Subject: Re: AMBER: DNA denatures during MD simulation

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Jul 23 2007 - 14:44:35 CDT


is it from imaging across the periodic box? try using the image
command in ptraj.
there have been lots of examples posted in the archives.

On 7/23/07, Prashanth Athri <athriprashanth_at_yahoo.com> wrote:
> Dear AMBER users:
> I ran a 50 ns (2500 frames) simulation with a ligand bound to the minor
> groove of DNA. Right at around 1350'th frame, DNA double strand denatures
> and immediately, in the next frame, they get back together. This
> 'phenomenon' repeats itself a couple of times till around the 1600'th frame,
> and then everything is back to normal.
> Any idea how this is happening?
>
> I would appreciate any input. Thanks in advance.
> Best,
> Prashanth
>
> ________________________________
> Looking for a deal? Find great prices on flights and hotels with Yahoo!
> FareChase.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu