VMD-L Mailing List

From: Ghalib Bello (ghalibbello_at_gmail.com)
Date: Mon May 05 2008 - 23:02:45 CDT

Hi all,
I am using NAMDENERGY to calculate the non-bonding interaction energy
between a solute and the atoms surrounding it. However, I am only interested
in the electrostatic component of the non-bonding interaction energy.
Therefore, I am setting the "*-pme*" parameter on, so that NAMDENERGY will
use PME to do the electrostatic interaction calculation. Because PME is not
a cutoff-based technique, what is the function of the 'cutoff' parameter in
this situation ? I was initially under the impression that, for PME-based
electrostatic energy calculations in NAMDENERGY, the 'cutoff' parameter has
no effect. In an attempt to confirm this assumption, I conducted a couple
tests, but I got some rather odd results, which I describe below.

My system is quite huge (94 X 94 X 180 cubic Angstroms), and the solute is
at the center. So I conducted the following test: I selected all solvent
atoms between 85 and 90 Angstroms away from the solute at the center of the
box. I then calculated the PME-based electrostatic interaction energy
between the solute atoms (*group1*) and the selected solvent atoms (between
85 and 90 Ang. [*group2*]). I did this calculation with the NAMDENERGY
"cutoff" parameter set to 12 A. Then I repeated the calculation, but with
the NAMDENERGY "cutoff" parameter now set to 90 A. I got very different
results:
Average (over dcd trajectory) electrostatic energy magnitude between *group1
* and *group2* atoms when NAMDENERGY "cutoff" parameter is set to 12 A =
0.67 kcal/mol
Average (over dcd trajectory) electrostatic energy magnitude between *group1
* and *group2* atoms when NAMDENERGY "cutoff" parameter is set to 90 A =
31.027 kcal/mol

Could anyone please explain the observed difference ? More importantly,
exactly how, and to what extent, does the NAMDENERGY "cutoff" parameter
influence PME calculations ?

Thanks,
Ghalib