AMBER Archive (2002)

Subject: who to address this to?...

From: Jessica Swanson (jswanson_at_mccammon.ucsd.edu)
Date: Sun Sep 08 2002 - 17:59:23 CDT

Hello,

I have three questions for you and I'm not sure just who they should be
addressed to. I apologize if I am inconveniencing the wrong people.

1. It seems that if imin=1 the standard coordinate and energy output
files are not written. I have imin=1, ntwx=300, and mtwe=50 but the
corresponding output files are empty.

2. I want to evaluate the internal energy of a single snapshot in vacumn.
I would like to use an infinite cutoff for the coulombic interactions. It
seems that there are two main ways of doing this. One is to implement
Anal. The other is to either do a single step of minimization of
simulation in sander. Anal would allow the infinte cutoff but would not
treat the system according to PME periodic boundary conditions. The
single step within Sander would not allow an infinite cutoff but would
treat the system according to PME/pbc. Do you have any further insight
as to how these two will result in different energies?

The current version of MMPBSA uses a single step of minimization. I would
like to know why this was chosen over a single step of simulation. It
seems to me that the latter would represent the energy of the ensemble
more accurately. And beyond the ability to break up the energetic
contirbutions of individual residues, which I believe sander can do, was
this switch from anal to sander chosen for any other reasons?

3. Finally, I am curious to hear if you have come up with an
equilibration protocol that seems ideal and applicable to most systems.

Thanks so much, these questions are difficult to address to anyone other
than the experts...:)

Sincere regards,

Jessica Swanson
McCammon Group
UCSD-Chem/Biochem
Urey Hall 4217
858-534-2916