Hello all,
I am a little curious as to which type of periodic simulation is preferred;
constand pressure or constant volume? In the amber6 manual they state that
this is a matter of preference, however, it seems that whenever I use
constant volume, my water box "floats" away. It is as though the density of
the system slowly decreases as the waters move further away from the solute.
I perform minimization and constant pressure equilibration to get a good
starting structure and density before running the production.
Most of the information I've read, including the online DNA tutorial on the
amber web site, uses constant pressure. Do you have any input for me?
Thanks,
Troy
-----Original Message-----
From: cheatham_at_cgl.ucsf.EDU]On Behalf Of
Thomas Cheatham
Sent: Friday, January 12, 2001 10:00 AM
To: Troy Bothwell
Cc: amber-faq_at_psc.edu; Thomas Cheatham
Subject: Re: Octahedral Box?
> Is an octahedral box recommended when doing simulations on DNA oligos
which
> are 10-20 base pairs? There is the potential for self diffusion of the
DNA
> so that the long axis of the DNA is along the short axis of the box.
Thanks
> for your comments.
The rotational diffusion time of a 10-20 base pair DNA is on the ns time
scale, therefore, it is expected that unless a force is added to prevent
rotation (which is only possible in current versions of AMBER either by
modifying the code to do this periodically, at the expense of a small
added torque, or via some positional restraints) the DNA will rotate. In
a long rectangular box for a long piece of DNA (> 10 base pairs) this will
be an issue since the long axis will rotate to the short axis of the box
and interact with periodic images.
Therefore, it does make sense to use a more "spherical" periodic unit cell
such as the truncated octahedron or rhombic dodecahedron (the latter of
which is not supported in LEaP yet), in my opinion. I do this routinely
when investigating larger systems.
Thomas E. Cheatham, III
Assistant Research Professor
Department of Medicinal Chemistry & Center for High Performance Computing
University of Utah INSCC 418
30 South 2000 East, Room 201 155 South 1452 East
Salt Lake City, Utah 84112-5820 Salt Lake City, Utah 84112-0190
cheatham_at_chpc.utah.edu
FAX: (801) 585-9119 FAX: (801) 585-5366
phone: (801) 587-9652
Received on Tue Jan 16 2001 - 13:28:04 PST
