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Date: Thu, 29 Mar 2001 16:19:54 +0800
From: shen Lingling <llshen@mail.shcnc.ac.cn>
To: "chemistry@ccl.net" <chemistry@ccl.net>
Subject: the solvate problem in EGO MD program
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Hi, I am using program EGO to do protein molecular dynamic simulation. In this program package, it add water molecular to the molecular surface of protein  with a certain thinkness. then the water were cut into spheric or cubic shape to get regular countier condition. After all that, my water sphere happened a density hetero-distribution during the following MD simulation. It even developed a vacuum hole at one side of the protein while water density on the other places are enhanced. Neither the total number of water molecular nor the shape of the water solution are changed. How is this happening and what will be the effects on the simulation? I will appreciate for any suggestion.


From chemistry-request@server.ccl.net Thu Mar 29 08:08:45 2001
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From: Patrik Johansson <patrikj@fy.chalmers.se>
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Dear CCLers

A hopefully simple problem:

I need to write the %RWF command line in G98 in more than one line
- the program cuts reading the line if it is too long - how to do this?
The reason for this is to split the RWF-file into many (>6) 2GB sized
files (32-bit).

If anyone from Gaussian has the answer so please reply.

best regards

/Patrik

-- 

Patrik Johansson
Scientist
Materials Physics
Chalmers University of Technology
patrikj@fy.chalmers.se

From chemistry-request@server.ccl.net Thu Mar 29 08:15:42 2001
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To: chemistry@ccl.net
Subject: g98 partial optimization with extrabasis
Date: Thu, 29 Mar 2001 15:16:08 +0200
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Dear all,

I tried to run a partial optimization fixing a dihedral angle,
with Gaussian 98 and using extrabasis. Unfortunately this
dihedral angle is never kept to its initial value. I did the same
calculation without extrabasis, and it ran fine. The geometry
was optimized with a frozen dihedral angle.
Any suggestion? Thanks in advance.

Christophe Jardin


From chemistry-request@server.ccl.net Thu Mar 29 05:45:48 2001
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From: "quantum" <quantum@orgchm.bas.bg>
To: <chemistry@ccl.net>
Subject: Workshop on Quantum Systems in chemistry and physics, 19-24 April, Sofia, Bulgaria
Date: Thu, 29 Mar 2001 13:46:25 +0300
Organization: Institute of Organic Chemistry, BAS
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There's still an opportunity to participate in the workshop! vm

========

THIRD ANNOUNCEMENT

 Sixth European Workshop on

 QUANTUM SYSTEMS IN CHEMISTRY AND PHYSICS

 19-24 April, 2001

 Sofia, Bulgaria

 Scientific Organizing Committee:
 E. Brandas (University of Uppsala) and H. Agren (The Royal Institute of
Technology, Stockholm), Sweden
 J. Stamenov and Ya. Delchev (Bulgarian Academy of Sciences, Sofia),
Bulgaria
 R. McWeeny (Universita di Pisa), Italy
 J. Maruani (C.N.R.S., Paris), France
 Y.G. Smeyers (C.S.I.C., Madrid), Spain
 S. Wilson (Rutherford Appleton Laboratory, Oxon), England

 Local Organizing Committee:
 R. Pavlov, Ya. Delchev, A. Kuleff, and P. Yotov (Institute of Nuclear
Research, Bulgarian Academy of Sciences, Sofia)
 V. Monev (Institute of Organic Chemistry, Bulgarian Academy of Sciences,
Sofia)
 A. Tadjer (Department of Chemistry, University Saint Kliment Ohridski,
Sofia)

 This Workshop, like those held in Pisa (1996), Oxford (1997), Granada
(1998), Paris (1999) and Uppsala (2000), will bring together chemists and
physicists interested in many-body quantum systems in molecular and material
sciences. The Workshop will include sessions on :

 * Density matrices and density functionals (DMF)
 * Electron correlation treatments: many-body methods and configuration
 interaction (ECT)
 * Relativistic formulations and effects (RFE)
 * Valence theory: chemical bond and bond breaking (VT)
 * Nuclear motion: vibronic effects, flexible molecules (NM)
 * Response theory: properties and spectra; atoms and molecules in strong
 electric and magnetic fields (RT)
 * Condensed matter: clusters and crystals, surfaces and interfaces (CM)
 * Reactive collisions and chemical reactions (RC)
 * Computational chemistry, biochemistry and chemical physics (CC)

 It is planned to publish the Proceedings of the Workshop in the
"International Journal of Quantum Chemistry".

 In 2001 the QSCP workshop will be held for the first time in an Eastern
European country, Bulgaria. Also for the first time, the workshop will see
the award of the "QSCP Promising Scientist" Prize, offered by CMOA. Full
details on the Workshop and the Award will be found on the web site:
http://www.inrne.bas.bg/quantum/

 The Workshop will be held in the Boyana Presidential Residence. The
Bulgarian Minister of Education and Science has granted special permission
to use these prestigious premises. His deputy, B. Toshev, has accepted our
invitation to open the workshop.
 Details of the venue, travel arrangements, registration costs and other
matters, as well as a registration form for the late registrants, can be
found on our workshop web page at http://www.inrne.bas.bg/quantum.

 ================


quantum  (Valentin Monev)
Local Organizing Committee
QSCP-VI workshop
http://www.inrne.bas.bg/quantum/

Institute of Organic Chemistry
Bulgarian Academy of Sciences
Sofia 1113, Bulgaria

email:quantum@orgchm.bas.bg
tel.:  (359 2) 979 6675, 9606 193
fax:   (359 2) 700 225
**********************************



From chemistry-request@server.ccl.net Thu Mar 29 09:06:50 2001
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From: "shen lingling" <shen_lingling@hotmail.com>
To: chemistry@ccl.net
Subject: solvate problem in EGO molecular simulation package
Date: Thu, 29 Mar 2001 14:03:46 -0000
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Hi,everyone:
I am using EGO package to do protein molecular dynamic simulation. It add 
water molecular on the molecular surface of protein with certain thinkness 
according to the surface shape of protein. then it cut the surrouding water 
into spheric or cubic shape (for simplier descripation of boundary 
condition).After all that, the water molecular desities in my simulations 
are homogeneous. But during my MD process, the water sphere developped a 
vacuum hole on one side of protein and the phenomenon is prevalent in all 
models of mine. Now I am just wondering how it is happening and what's 
effect it bringing in? I am waiting for any suggestions and discusses.


Lingling Shen
_________________________________________________________________________
Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com.



From chemistry-request@server.ccl.net Thu Mar 29 10:23:18 2001
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Date: Thu, 29 Mar 2001 07:23:17 -0800 (PST)
From: kara_hulya@yahoo.com
Subject: Cu-Gd
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Dear CCL,

I'm trying to use G98 to calculate exited state
energies for a Cu-Gd dimer
I'm having trouble with the multiplicity of the dimer.
Could you tell me please What can I do?

I am looking forward your answer.
Best Wishes
Hulya KARA    

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From chemistry-request@server.ccl.net Thu Mar 29 11:13:52 2001
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Date: Thu, 29 Mar 2001 18:13:48 +0200
To: Patrik Johansson <patrikj@fy.chalmers.se>
From: Christoph van =?iso-8859-1?Q?W=FCllen?=  <Christoph.vanWullen@tu-berlin.de>
Subject: Re: CCL:G98 %RWF
Cc: chemistry@ccl.net
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>Dear CCLers
>
>A hopefully simple problem:
>
>I need to write the %RWF command line in G98 in more than one line
>- the program cuts reading the line if it is too long - how to do this?
>The reason for this is to split the RWF-file into many (>6) 2GB sized
>files (32-bit).
>
My advice is to make the rwf-filenames very short, so that many of them
fit into one line. As far as I recall, there is no other solution.
-- 
+---------------------------------+-------------------------------------+
| Prof. Christoph van Wullen      | Tele-Phone (+49) (0)30 314 27870    |
| Technische Universitat Sekr. C3 | Tele-Fax   (+49) (0)30 314 23727    |
| Strasse des 17. Juni 135        | eMail                               |
| D-10623 Berlin, Germany         | Christoph.vanWullen@TU-Berlin.De    |
+---------------------------------+-------------------------------------+

From chemistry-request@server.ccl.net Thu Mar 29 11:01:07 2001
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Date: Thu, 29 Mar 2001 08:01:05 -0800 (PST)
From: Max Valdez <maxvaldez@yahoo.com>
Subject: Protocol error in NWCHEM ?
To: chemistry@ccl.net
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Dear CCL'ers

I'm trying to run NWChem on an AMD cluster with RH6.2
kernel 2.2.16-22smp 

Well, when I try to run parallel I get the next error

bash$ parallel processors nwchem3.nw > nwchem3.out2
poll: protocol failure in circuit setup
  2: interrupt(1)
bash$   

I have rhosts file set correct (I think) because I
actually can rlogin to any of the nodes in the cluster
without password

Would anybody be so nice to give me some advice on
this?? I only have been able to run on multiprocessors
in a 4 CPU cluster on a quadruple processor
motherboard.

Another question, is it possible to run NWChem
distribuited on different architectures??

Thanks in advance !
Max


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From chemistry-request@server.ccl.net Thu Mar 29 15:00:05 2001
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From: "Alexei Khalizov" <khalizov@chemistry.mcgill.ca>
Organization: Chemistry Dept., McGill University
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>Dear CCLers
>
>A hopefully simple problem:
>
>I need to write the %RWF command line in G98 in more than one 
line
>- the program cuts reading the line if it is too long - how to do this?
>The reason for this is to split the RWF-file into many (>6) 2GB 
sized
>files (32-bit).
>
>My advice is to make the rwf-filenames very short, so that many 
of them
>fit into one line. As far as I recall, there is no other solution.

Yes, and if it is a Windows version of Gaussian, use short input 
and output file names as well as short folder names. I had a lot of 
troubles with %RWF command and I believe I resolved most of 
them. According to the Gaussian manual/help the %rwf line length 
is limited by 120 characters. Actually, it is well shorter when 
Gaussian refuses to function. Explanation is simple - G98w 
creates a file "GXX-Exec.Dat" containing only one line describing 
the job, and this line is limited by 255 characters:
{
     l9999.exe 10485760 "c2h6.chk" 1 "gxx.int" 0 "gxx.rwf" 0 
"gxx.d2e" 0 "gxx.scr" 0 "d:\qchem\G98W\Scratch\gxx.inp" 0 
"D:\Qchem\G98W\Project2\Inertia moment\c2h6_Tight1.out" 0
} 
If one exceeds the length limit, various things may happen. For 
example, the output file name may be cut and the output will be 
split among three files with strange names. These names depend 
on position of cutting:
{
D:\Qchem\G98W\Project2\Inertia moment\c2h6_Tight1.out
D:\Qchem\G98W\Project2\Inertia moment\c2h
or even
D:\Qchem\G98W\Pr
}
If the name is cut completely or it doesn't follow OS rules 
("D:\Qchem\G98W\") Gaussian terminates with an error. 

There is a case which I still cannot explain: I successfully 
completed calculation using 6-311+G(3df) basis set. I arranged five 
rwf files 240mw each and MaxDisk=1200mw. Four of five rwf files 
were occupied completely and the last one - in half. When I 
reduced the basis set to 6-311G(2df) and ran the input file from a 
different folder, G98w occupied ALL rwf files and terminated with an 
error. I added one more rwf file without changing MaxDisk 
(1200mw) and re-ran calculation - all rwf (6) were again occupied. 
Finally, I shortened ALL file names (i.gjf, i.out, i.chk) and moved 
the input file to the root directory. This action resolved the problem -
 only three rwf files of nine are occupied and the job is being 
processed!

Alex


-------------------------
Dr. Alexei Khalizov
Department of Chemistry
McGill University,
801 Sherbrooke St. W.,
Montreal, Quebec, CANADA,
H3A 2K6

Phone: (514) 398-6920
Fax: (514) 398-2382

From chemistry-request@server.ccl.net Thu Mar 29 13:36:20 2001
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Drr Sirs.
I am running G94 with the SCIPCM model performing a frequency calculation with no optimization
of an heterocycle molecule. Unfortunately, as the calculation takes several days,
the rogram stops dur to problemas with the machine. I have been trying to restart the expensive 
calculation with the instructions

#P BP86/GEN SCF=sleazy SCRF=SCIPCM Freq=(Numer,Restart)

78.39 0.01287017615

These two last numbers are the water dielectric constant and the isodensity value.
Nevertheless the program starts where it stopped using the old .chk file, it gives
the following message

> Cycle   1  Pass 0:
>  Symmetry not used in FoFDir.
>  MinBra= 0 MaxBra= 2 MinRaf= 0 MaxRaf= 2.
>  IRaf=       0 NMat=   1 IRICut=       1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0.
>  End of File Reading Reaction Field Parameters.
>  Error termination via Lnk1e in /usr/local/g94/l502.exe.
>  Job cpu time:  0 days  0 hours  1 minutes 31.7 seconds.
>  File lengths (MBytes):  RWF=    9 Int=    0 D2E=    0 Chk=    4 Scr=    1
>

Does anybody know how can I start the job???

Thanks a lot for your help

Yours sincerely

Dr. Maria Eugenia Costas Basin
Faculatd de Quimica, UNAM.
Mexico
e-mail: costas@zenon.pquim.unam.mx






From chemistry-request@server.ccl.net Thu Mar 29 23:16:53 2001
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To: CompuChem List <chemistry@ccl.net>
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Hi,
  could anybody sughgest sources on the Net where I could get information
regarding paralell processing (programming, algo's, hardware setup etc)
with an emphasis on quantum chemistry

TIA,

------------------------------------------------------------------------
Rajarshi Guha                       | He who fears the unknown may one
Dept. of Chemistry		    | day flee from his own backside.
IIT Kharagpur.                      |
		                    |                -- Sinbad
email: rajarshi@presidency.com      |
       rajarshi@cts.iitkgp.ernet.in |
web  : www.psynet.net/jijog         |
-------------------------------------------------------------------------



From chemistry-request@server.ccl.net Thu Mar 29 23:20:09 2001
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To: CompuChem List <chemistry@ccl.net>
Subject: Metal Force Fields
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Hi,
  some time  ago I had posted a question regarding force fields for
metals. The question was:

>Hi,
>could anybody point me to reviews/links of force fields for metallic
>systems - I'm more interested in the nature of the force fields themselves
>rather than the applications to specific systems.

I recieved several very informative replies which I have summarised below.
(This mail may have been posted previously)

###############################################################################

From: Isaac B. Bersuker <bersuker@ne059.cm.utexas.edu>
Date: Tue, 13 Mar 2001 11:24:14 -0800

You are correctly rising the question of the nature of force fields for metal
containing systems because, strictly speaking, there are no general force fields
in these cases. See my book by Wiley, New York, 1996, maybe you will find
something of interest with regard to your question.
Isaac Bersuker

--
Dr. Isaac B. Bersuker
Institute for Theoretical Chemistry
Department of Chemistry & Biochemistry
The University of Texas at Austin
Austin, TX 78712, USA
Ph: (512) 471-4671
Fax: (512) 471-8696
Email: bersuker@eeyore.cm.utexas.edu

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Date: Tue, 13 Mar 2001 19:25:12 +0100
From: Jeremy Greenwood <jeremy@compchem.dfh.dk>

This sounds like a question for which Per-Ola Norrby would be a good
person ask.
Email: pon@kemi.dtu.dk (alt. peo@compchem.dfh.dk)
His recent review is "Co-ordination Chemistry Reviews 212 (2001) 79-109

HTH

Jeremy
----------------------------------------------------------------------
Jeremy Greenwood                                 jeremy.greenwood@i.am
Department of Medicinal Chemistry                      bh +45 35306117
Royal Danish School of Pharmacy                        fx +45 35306040
Universitetsparken 2, DK-2100 Copenhagen, Denmark      ah +45 32598030
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              'Any excuse will serve a tyrant.' -- Aesop
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Date: Tue, 13 Mar 2001 20:25:09 +0100
From: Per-Ola Norrby <pon@kemi.dtu.dk>

	The second edition of "Molecular Modeling of Inorganic
Compounds" by P. Comba and T.W. Hambley just came out (I got it
today).

	Also, try these as leads:

"Deriving Force Field Parameters for Coordination Complexes"
Per-Ola Norrby and Peter Brandt, Coord. Chem. Rev. 2001, 212, 79-109

"Recipe for an organometallic force field"
Per-Ola Norrby, in Computational Organometallic Chemistry, Ed: T.
Cundari; Marcel Dekker: New York, 2001, 7-37

	Best,

	Per-Ola Norrby
-- 

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/
Technical University of Denmark, Dept. of Chem., Org. Chem.
Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
tel +45-45252123,  fax +45-45933968
Email: pon@kemi.dtu.dk (alt. peo@compchem.dfh.dk)

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Date: Tue, 13 Mar 2001 23:15:39 -0500
From: David White <whitedp@uncwil.edu>

Raj,

There is an excellent book coming out edited by Tom Cundari called
"Computational Organometallic Chemistry", which will give you many
references (Marcel-Dekker).  Also, there is a book by Peter Comba, which has
some parameters.  I have parameters for Cr and Rh.  Tony Rappe has also
written a book called Molecular Mechanics Across Chemistry (I think),
published by University Science Books.

Hope this helps,

Dave

**********************************************************************
David P. White, PhD               Phone: (910) 962-7499
Assistant Professor                  Fax: (910) 962-3013
Wilmington Institute for the Structural Design of
Organometallic Materials (WISDOM)
Department of Chemistry
University of North Carolina at Wilmington
601 South College Road
Wilmington, NC 28403

http://aa.uncwil.edu/wisdom

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Date: Wed, 14 Mar 2001 12:47:27 -0500
From: Shyam Vyas <svyas@msi.com>

Hi Rajarshi,

The classic metal forcefield is the Sutton-Chen potential.

A.P. Sutton and J. Chen  Phil. Mag. Lett., 61, 139 (1990)

The GULP simulation code has a library of these parameters,
the following link may be of use to you.

http://www.ch.ic.ac.uk/gale/Research/gulp.html#Overview

Also you should look at the work of David Bacon at
University of Liverpool.

http://www.liv.ac.uk/mateng/research/research_98/metals.htm

Cheers,
Shyam

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Date: Thu, 15 Mar 2001 03:24:08 -0800
From: Darren Fayne <fayned@lycos.com>

Hi Rajarshi,
  Here is a few reviews that I'm sure will be of interest to you.
(a) Brubaker, G.R. and Johnson, D.W., Coord. Chem. Rev., 1984, 53, 1-36;
(b) Hancock, R.D., Progr. Inorg. Chem. 1989, 37, 187;
(c) Landis, C.R., Root, D.M. and Cleveland, T., Molecular mechanics force fields
    for modeling inorganic and organometallic compounds, "Reviews in Computational
    Chemistry", Lipowitz, K.B. and Boyd, D.B., (Eds.) Vol. 6, 1995, p. 73-148;
(d) Hay, B.P., Coord. Chem. Rev., 126, 1993, 177-236;
(e) Comba, P., Coord. Chem. Rev., 1999, 185-186, 81-98.
  Enjoy the reading.....
Darren


---
Darren Fayne
School of Chemical Sciences,
Dublin City University,
Dublin,
Eire.

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Dept. of Chemistry		    |  kiss, you get Kafka dreams."
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