AMBER Archive (2003)

Subject: adjust virial

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Tue Feb 25 2003 - 02:15:45 CST

Hi amber users,

I am trying to understand what are the components that PME writes out when
one sets the VERBOSE parameters to higher values (eg 3). The reason is
that I get the value of EEL equal to NaN.
I did look at the Essmann paper on PME, searched through the archives in hope to find
a little bit more information and looked into the code (especially the
ew_force.f one). I have the following questions:

1. I get in my output that Ecoulomb = NaN. According to the code, this is
stored in eelt and is equal to the sum of the Electrostatic components
self (ees), reciprocal (eer), direct (eed) and adj (eea). Out of these
components the only one I get NaN is eea which is calculated as cgi*cgj/r.
The NaN must then be pointing to the fact that two charges are overlaping
(r=0, 1/r=NaN)?? I looked into my pdb file but none of the atoms in my
system seem to overlap. There are bad contacts but I was expecting that
the minimizer (once there is a big force between to charges/atoms) should
be able to move the atoms so that it would minimize these forces.

2. I also get a NaN value for the components of the Adjust Virial
(adj_vir) but I could not trace this down as how it is calculated. I am
guessing that this is a correction term? If yes, how is it calculated?

3. What is conceptually the difference between the atomic and molecular
virial? From the code it seems that the molecular virial (molvir) is the
real virial (frc*xr -force *coordinate).

4. What is the self virial (self_vir) and how it is calculated?

If I may have a suggestion perhaps it is a good idea to include a good
explanation of the PME implementation in amber under FAQ? Sometimes it is
difficult to trace down from the code all the details of the calculations.

Thank you in advance for your help,
Ioana