Subject: G98: Massage and %Chk

From: The Matt <[email-masked]>
Date: 10 Apr 2002 12:36:31 -0600

I feel kind of dumb for asking this, but I can't seem to get Gaussian to
do what I want, and it's probably pretty simple.

Namely, I am trying to do some BSSE jobs all in the same input file.  (I
have access to Rev. A.7, so I can't use the Counterpoise keyword.) 
Naively, I try this:

%Chk=trial.chk
# B3LYP/STO-3G SCF=(QC,Tight) Opt=ModRedun NoSymm
...molecule spec, doing Cl-...CO2, this job for opt....

--Link1--
%Chk=trial.chk
# B3LYP/STO-3G SCF=(QC,Tight) Massage Geom=Check
...Cl- nucleus zeroed, use optimized geom from above...
1 Nuc 0.0

--Link1--
%Chk=trial.chk
# B3LYP/STO-3G SCF=(QC,Tight) Massage Geom=Check
...Zero out CO2, want to use OPT geom from two steps ago...
2 Nuc 0.0
3 Nuc 0.0
4 Nuc 0.0

So, the first two steps work great.  But the third explodes since in
reading the checkfile, it also reads that the Cl nucleus is Massage-d to
zero.  So, the second Massage rubs out all the nuclei, and hilarity
ensues (hilarity=segmentation faults, crashes, &c.)!

How can I get it so that Gaussian reads the original optimized structure
in both BSSE steps, without it transferring the first Massage to the
third step?  (Essentially, make trial.chk read-only after the first
step.)  Or will I be doing this in three jobs instead?

Thanks,
Matt Thompson
-- 
"And isn't sanity really just a one-trick pony, anyway?  I mean,
all you get is one trick, rational thinking, but when you're good
and crazy, ooh ooh ooh, the sky's the limit!" -- The Tick
  TheMatt -- http://ucsub.colorado.edu/~thompsma/Home.html

---

From: Pedro Salvador Sedano <[email-masked]>
Date: Thu, 11 Apr 2002 01:51:59 +0200

Dear MAtt

I think the best solution will probably be to MASSAGE the Cl atom in the 
last calculation too..back to it's original charge

1 nuc 17.0

Pedro

-- 
--------------------------------------------------------------------
Pedro Salvador Sedano
Ph.D. Student                             I'll stare the sundown,
Institut de Quimica Computacional         untill my eyes go blind.
Universitat de Girona                     I won't change direction,
Campus Montilivi 17071, Girona,Spain     and I won't change my mind.
iqc.udg.es/~perico
--------------------------------------------------------------------

---

From: "J. Zheng" <[email-masked]>
Date: Wed, 10 Apr 2002 16:49:41 -0700 (PDT)

Dear CCLer:

  I have a general question about the protein simulation. For protein
simulation, force field is important issue. As I know as far, most of
persons use different force fields such as Charmm, Gromas, Amber etc to
describe different protein systems with all-atoms model.

  Sometimes protein is so huge that we have to consider another way to
deal with it. For example, we introduce new algorithm (Cell multipole
method, PPPM) to reduce computation time, or we resort to  parallel
program.  I am curious
that does anyone has develop the general force field (epslo, sigma,
charge) for only 20 acid amio residues if we treat each residue as
one atom.  If yes, could you please give me a reference
paper?

   Now I am working on one protein simulation. I was just thinking about
which way I should go.

   I will appreciate for any suggestion.

   good day.

   jie
-----------------------------------------------
|  JIE ZHENG                          	      |
|  Department of Chemical Engineering	      |
|  University of Washington		      |
|  Seattle, WA 98105, USA   		      |
-----------------------------------------------
|  Tel:  (206) 616-6510 (o)		      |
| Email: [email-masked]	      |
| Webpg: students.washington.edu/jzheng73     |
-----------------------------------------------