From chemistry-request@ccl.net Mon Mar 9 00:11:33 1992
Date: Sun, 8 Mar 1992 23:13 EST
From: "DOUGLAS A. SMITH" <FAX0236@uoft02.utoledo.EDU>
Subject: burning time on supercomputers
To: chemistry@ccl.net
Status: R
In response to Jan Labanowski's question, we have one area which still
seems to defy current resources, or at least pushes them to the extreme.
We have been studying hydrogen bonding in a series of di- and triamides
which involve from 8 to 20+ heavy atoms, using molecular mechanics to
probe the potential energy surface (you guessed it- the multiple minimum
problem).
We are now at the stage of beginning to take our tens of minima for each
compound, found using the AMBER force field in MacroModel, and submitting
each for ab initio single point and geometry optimization. Hydrogen
bonding requires massive basis sets for molecules of this size - a recent
paper by Pople suggested that RHF/6-31+G** was a minimum requirement,
although they did their optimizations at RHF/6-31G* single points at
MP2/6-31+G**. We want to also do RPAC calculations of NMR spectra and
chemical shift tensors, so the wavefunction must be a good one. These
last few requirements are not trivial in and of themselves, but when
coupled with 8-10 compounds with from 5-40 minima each, the need for
resources just explodes.
Regardless, we are trying.
Doug Smith
Assistant Professor of Chemistry
The University of Toledo
Toledo, OH 43606-3390
voice 419-537-2116
fax 419-537-4033
email fax0236@uoft02.utoledo.edu
From chemistry-request@ccl.net Mon Mar 9 11:26:19 1992
Date: Mon, 9 Mar 1992 09:23 EST
From: "DOUGLAS A. SMITH" <FAX0236@uoft02.utoledo.EDU>
Subject: basis sets for hydrogen bonding
To: chemistry@ccl.net
Status: R
I have already received several requests for the Pople reference I
mentioned in my posting about burning supercomputer time. Here it is:
Head-Gordon, T.; Head-Gordon, M.; Frisch, M. J.; Brooks,
C. L. III, Pople, J. A. J. Am. Chem. Soc. 1991, 113,
5989-97. The paper is titled "Theoretical Study of
Blocked Glycine and Alanine Peptide Analogues."
I also thought I would pass along this note from Janet Del Bene, who
has done a tremendous amount of work on hydrogen bonding, particularly
in small molecules such as, but not limited to, HF. Note that if you
take Janet's suggestion, my problem gets _much_ larger.
Doug Smith
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>Doug,
> I was interested to see your comment on the hydrogen-bonding
>model. You might be interested in a paper that I am giving at
>Sanibel which suggests that geometry optimization at MP2/6-31+G(d,p)
>is required, followed by single-point MP4/cc-pVTZ+ single-point
>energies. (In some cases, MP2 is okay for the energetics as well,
>but a very large basis is needed.) Regards, Janet
From chemistry-request@ccl.net Mon Mar 9 11:29:30 1992
Date: Mon, 9 Mar 1992 10:09:50 -0500
From: jkl@ccl.net
Subject: Re: Identification of referees
To: chemistry@ccl.net
Status: R
Forwarding to the list
---------- Begin Forwarded Message ----------
Date: Mon, 9 Mar 1992 9:44:02 -0500 (EST)
From: EDELSON@EVAX12.ENG.FSU.EDU (Dave Edelson)
Subject: Re: Identification of referees
To: chemistry-request@ccl.net
Most scientific journals maintain the identification of referees as
confidential information, they are not known even to the authors
unless the referee gives permission.
To change this would involve a major rethinking of the entire review
process, and I suspect it would become much more difficult for
journals to obtain objective reviews for their contributions.
David Edelson, Editor
Computers and Chemistry
----------- End Forwarded Message -----------
From NU145752@VM1.NoDak.EDU Mon Mar 9 15:41:59 1992
Date: Mon, 09 Mar 92 14:41:18 CST
From: Jan Jensen <NU145752@VM1.NoDak.EDU>
Organization: North Dakota Higher Education Computer Network
Subject: Postscript on the Mac
To: chemistr@ccl.net
Status: R
Fellow Netters,
This is a question for all you Mac users. Is there a Mac program out
there that will take a post script file and render a picture on the
screen that one can cut and paste? Our graphics codes produce post
script files for hard copies but it would be nice to edit the pictures on the
Mac before printing. Any held will be greatly appreciated.
Jan H. Jensen
Dept. of Chemistry
North Dakota State University
Fargo, ND 58105
========================================================================
5
LINE 1 %DATE
LINE 4 %SUBJ
LINE 5 %END %IDEND %IDSTART
LINE 6 %DIV
LINE 25 V900101 %RESUME
A question for Mac Users
chemistry
ccl.net
0
11
8 61
1
0 0 1 1 0
1 0 0 0
25
From chemistry-request@ccl.net Mon Mar 9 18:08:57 1992
Date: Wed, 5 Feb 92 00:56:57 -0500
From: wampler@bchiris.biochem.uga.EDU (John Wampler)
Subject: CM-5
To: chemistry@ccl.net
Status: R
Does anyone have information about the suitability of the Thinking Machines
CM-5 for running computational chemistry programs. We are interested in
both quantum chemistry and molecular mechanics based calculations (not
Monte Carlo). Does anyone have benchmarks that would indicate the % peak
performance that might be expected for such codes. Please reply
direct to wampler@bchiris.biochem.uga.edu
Thanks in advance.. JW
From chemistry-request@ccl.net Mon Mar 9 20:12:58 1992
Date: Mon, 9 Mar 92 18:22:54 -0500
From: jle@world.std.COM (Joe M Leonard)
Subject: Request for comment
To: chemistry@ccl.net
Status: R
Another along the lines of computationally-intensive cal'n...
Since we're in the middle of an explosive growth in computational
power (particularly with the advent of mpp machines), I'm curious
as to whether it's time to rethink non-bonded cutoffs in MD cal'n.
Isn't the physics better if infinite cutoffs are used, and doesn't
the force fields get a little easier to parameterize?
I'd appreciate folks' thoughts on the matter - directly or via the
net. I seem to recall hearing talks on these ideas over the last
few years - but I've been wrong before. Restated, are cutoff's
VAX-like code remnants (like indirect lists replacing sparse matrices)
that should be replaced when one gets the chance?
Joe Leonard
jle@world.std.com
From chemistry-request@ccl.net Mon Mar 9 20:16:45 1992
Date: Mon, 9 Mar 92 19:02:51 EST
From: "Michael A. Lee" <lee@nematic.kent.EDU>
Subject: An opinion on referee identification
To: chemistry@ccl.net
Status: R
Having just read the e-mail of David Edelson, Editor
Computers and Chemistry, I am a little surprized that
there has been so few comments on this subject.
Presumably this is not a question of anonymity. I assume
a rejected paper would not result in the name of the
referee being given to the authors.
I suspect this is an issue on Quality. Would you as a referee
be willing to put your name on a piece of junk? Would you
as a referee make the kind of inane comments which are made
by some referees if you knew that your identity would become
public?
Actually, it sounds like a good idea to me. I predict that
I would have fewer and higher quality articles filling the
volumes in my library.
Mike Lee
Physics, Kent State