Re: who to address this to?...

From: Michael Crowley <>
Date: Mon 9 Sep 2002 10:41:16 -0700

> 2. I want to evaluate the internal energy of a single snapshot in
> I would like to use an infinite cutoff for the coulombic interactions.
> 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?
You can run vacuum simulations (nonperiodic) with sander in amber7
with whatever cutoff you would like within reason. In particular,
as Holger suggests, you need only choose a cutoff that will
be larger than the longest distance between atoms in your system
during the entire simulation. I only wanted to add that I would
not suggest 9999 A since sander will try to make a grid of
little cells to fill the space needed for a cutoff that large and
you will run out of memory. I suggest that you choose at most
a cutoff that is twice the size of your system.

The variables you want to use are:
in &cntrl nameist
   cut=<your chosen cutoff>

in &ewald
   eedmeth=4 or 5 (4 for straight coulomb, 5 for dist dep diel)

When you specify ntb=0, PME is turned off.
The eedmeth is in &ewald for historical reasons, it will not
turn on PME, only say how the electrostatics should be treated.
Once you have chosen these variables, you should be able to
do minimization and MD in your normal way.

You can do PME pbc calculations on the system if you want using
very large boxes, but I am not sure what you find out from that
simulation. I suggest giving the above method a try first.


Physical mail: Dr. Michael F. Crowley
                 Department of Molecular Biology, TPC6
                 The Scripps Research Institute
                 10550 North Torrey Pines Road
                 La Jolla, California 92037

Electronic mail:
Telephone: 858/784-9290
Fax: 858/784-8688
Received on Mon Sep 09 2002 - 10:41:16 PDT
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