Subject: QCOR in PME (CHARMM)

From: Marcin Krol <[email-masked]>
Date: Mon, 10 Jun 2002 17:15:20 +0200 (METDST)

Dear Charmm Users,

I've tried to set up PME calculations of a neutral system (protein in
water with counterions) and I'd like to know if I should bother about QCOR
keyword (it should be reduced or set to zero for periodic systems in
solution - that's what a manual says) or not. Is QCOR a net-charge
correction (as described in the JCP 108, 7070 paper) keyword and it is
ignored in neutral system simulation?
I've also encountered another problem when doing paralell PME
calculations. My job runs on two and four processors but fails to run on
three. I get non 2**N PE count in transpose error, but my FFT value is 64
in each direction. Is there any way to force it run on three procs or not?

Thank you in advance
Marcin Krol

---

From: "Telkuni" <[email-masked]>
Date: Tue, 11 Jun 2002 01:46:15 +0900

Hello CCLers,

I have sent a question about Extended Huckel MO(EHMO) last week.
Although there was only one reply, it is very available.
(Thank you Dr.Lewars !)
Here I send it again.

  ...Now, do you know the web site "Scirus http://www.scirus.com/"?
   The site was introduced by Dr.Shobe. Very useful!

---------------------------------------------------
     Telkuni Tsuru     [email-masked]

--- Original question ---
> Hello CCLers,
> 
> I have read the explanation of Extended Huckel MO(EHMO) method 
> on one book (Sorry, it is Japanese!)
> 
> It said "EHMO isn't SCF, so it isn't available for the systems which have the 
> polarizability, especially not for the polypeptides. "
> But, I saw some examples of other articles on which EHMO have been applied 
> to polar-systems.
> 
> So I like to know the systems which are suitable or not-suitable for EHMO.
> 
> I will summarize the responses.
> 
>     Thanks in advance.

--- Reply ---
Hello,

An extended Hueckel method calculation can be run on *any* molecule. However, the
EHM gives only qualitative, not quantitative, results. It is very poor for
optimizing geometries, so an experimental geom or maybe a molecular mechanics
geom is used as input. Relative energies of isomers from the EHM are not very
good either. The main use of the EHM is to get the shapes and the ordering of
energies of molecular orbitals; with good intuition this can be useful. EHM
calculations are done mostly on polymers and "extended systems", i.e. solids.
Physicists, Professor Hoffmann tells me, are always rediscovering the method.

(The EHM is not SCF because the Fock matrix elements do not require an initial
guess of the basis set coefficients; the Fock matrix thus does not have to be
refined iteratively).

For a good brief account and references, see I. N. Levine, "Quantum Chemistry",
Prentice Hall, 2000.

E. Lewars
=====