VMD-L Mailing List

From: Abolfazl Bayat (abolfazl.bayat_at_gmail.com)
Date: Mon Jun 25 2012 - 11:16:49 CDT

Dear vmd users,

I try to compute the electrostatic potential of my system at certain
points. I use "pmepot" and the output of this function is saved as a DX
file. I have some questions as in the following:

1) What is the potential that is computed by this function. I need to have
both the Coulomb and van der waals potential as the output. Does it compute
both or only Coulomb potential?

2) If I select some part of my system, does it mean that the potential of
just only that part is computed and the rest is ignored?

3) In the "pmepot plugin help", it has been written that the charge
information must be available. However, I load PSF file + my DCD file. Do I
need to specify anything more?

4) How can I get the potential at just certain locations instead of the
whole periodic cell? Currently the size of the output file is large and I
get weird results for my potential.

Thanks for your help,
Abolfazl Bayat