AMBER Archive (2003)

Subject: RE: MD problem

From: Yong Duan (yduan_at_udel.edu)
Date: Thu May 29 2003 - 19:58:21 CDT

I'd agree with Guanglei's assessment.
Your 1 fs time step is about half of what was required to run a stable
MD simulation on a regular DNA-water system with PME. For this reason
along, your simulation should be about one order of magnitude more
stable than the typical simulations.
It may be a good idea to check the geometry (bond, angle, etc) of the
adduct. It appears that the adduct were in close contact with the base.

yong

-----Original Message-----
From: Guanglei Cui [mailto:cuigl_at_morita.chem.sunysb.edu]
Sent: Thursday, May 29, 2003 5:28 PM
To: Shuang Ding; cuigl_at_ilion.bio.sunysb.edu
Cc: amber_at_heimdal.compchem.ucsf.edu
Subject: Re: MD problem

are they close or interacting with the adduct? does your protocol work
with
regular DNA? if yes, then i would check if the adduct is properly setup.

On Thursday 29 May 2003 17:30, Shuang Ding wrote:
> Hi, the atoms 172 and 173 are on the adjacent base next to that
adduct.
> 

-- 
Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790