Subject: DelPhi questions

From: "Dmitry M. Medvedev" <[email-masked]>
Date: Wed, 12 Jul 2000 21:43:06 -0700

Dear netters,

I am trying to make certain calculations using DelPhi distributed by MSI,
release 97.2. I've run into some problems I can't solve. Here they are:

1. When I don't center the grid on the center of the molecule, then the site
potential file (file.frc) is completely screwed up, showing ridiculous values
of potential and total electrostatic energy. Why is it so?

2. The values of total electrostatic energy reported in log file and in site
potenial file are different. This difference is small if I center the grid on
the center of the molecule, and is large if the center of the grid is far from
the center of the molecule. What is the reason for this difference?

3. The convergence criterion does not seem to work. When I changed energy
convergence criterion from 0.000001 to 0.1, nothing changed in the calculation.
How can I make this criterion work?

4. What do centers of assigned positive and negative charges in grid units (gu)
reported in log file mean?

5. What are the values of potentials given in the log file?

6. I was trying to calculate (as a test) the change of energy of an ion when I
changed its radius from 1.35A to 9.35A. I used grids centered on the ion with
grid steps from 1A to 0.02A, using focussing boundary conditions. The charge of
ion was 1e, the internal dielectric permeability was 4, the external dielectric
permeability was 80. I found that when the grid step was in the range
approximately from 0.2A to 06A, the desolvation penaly was close to the correct
value (42.1kT with T=298K), but for smaller values of the grid step is started
to deviate from this value. Why does it happen?

7. Could anyone explain what DelPhi does with spectral radius? I don't
understand what is written in the manual.

Thanks in advance,
Dmitry