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To: Ramiro Arratia Perez <raperez@valdivia.uca.uach.cl>
From: hebant@ext.jussieu.fr (Pascal HEBANT)
Subject: Re: CCL:II Workshop of Computational Chemistry..
Cc: chemistry@www.ccl.net


Dear Sir,
I read your annoucement for the II Workshop of Computational Chemistry and
molecular spectroscopy.

We are interested in participating but can you send me more details about
the program

Regards

Pascal



*****************************************************************************
Pascal HEBANT

Laboratoire d'Electrochimie et de Chimie Analytique
Ecole Nationale Superieure de Chimie de Paris
11 rue Pierre et Marie Curie                            75005 Paris FRANCE

tel:+33 - 01 44 27 66 94                             fax: +33 - 01 44 27 67 50
http://alcyone.enscp.jussieu.fr/Pages/LECA/Electrochimie.html
*****************************************************************************



From ap16390@ggr.co.uk  Thu Oct 24 05:31:43 1996
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Date: Thu, 24 Oct 1996 10:17:44 GMT
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To: chemistry@www.ccl.net
Subject: SUMMARY - roto-matrix -


Dear Netters,


	Here is the summary and the original message concerning
roto translations.
An easy solution to the problem is to use/look the quaternion-fit program
as suggested by David Heisterberg, while for theory I found all the other
contributions very interesting.

	Thank you very much for your help

-Alfonso


###############
Initial Posting
###############

Dear Netters,

	I would like to ask for an expertise about linear transformations
performed via rotational matrixes.

	Given the 3D coordinates of three points P1(xyz) P2(xyz) and P3(xyz)
in their initial (T0) and final (T1) position. Which is the best way
for calculating the rotational matrix and translation capable of such
transformation ? (distances between the three points are constants so we
can consider it "rigid" between each others)

	Any help and or information is very welcome and I will summarize
your contributions.


	Yours sincerely

	-Alfonso Pozzan


#############
   ANSWERS
#############

#####################
From:     Jan Reimers
#####################

Without the translation its a simple 3x3 system of equations.  Let p1, p2,p3
be the original 3 coordinate vectors and p1', p2' p3' be the transformed
vectors.  Then

[p1x' p2x' p3x']      [r11 r12 r13][p1x p2x p3x]
[p1y' p2y' p3y']   =  [r21 r22 r23][p1y p2y p3y]
[p1z' p2z' p3z']      [r31 r32 r33][p1z p2z p3z]

Or in matrix notation

p' = Rp

and so R = p' * inverse(p)

Note that R must be unitary if it is a rotation matrix.  In general R can
contain dialations as well, this is determined completely by your p and p'
vectors.

Now to add the translation you will need 1 more vector, and expand
to the problem to a 4x4 system

[p1x' . . p4x']     [      Tx] [p1x . . p4x]
[ .   . .  .  ]  =  [  R   Ty] [ .  . .  . ]
[ .   . .  .  ]     [      Tz] [ .  . .  . ]
[ 1   1 1  1  ]     [0 0 0 1 ] [ 1  1 1  1 ]

Now solve the 4x4 system to get R and T.

Hope this helps


+--------------------------------------+-------------------------------------+
| Jan N. Reimers,  Research Scientist  | Sorry, Don't have time to write the |
| Moli Energy (1990) Ltd. B.C. Canada  | usual clever stuff in this spot.    |
| janr@molienergy.bc.ca                |                                     |
+--------------------------------------+-------------------------------------+

#########################
From:     Dr Mark J Biggs
#########################

Hi Alfonso,
	for transformation matricies around axes or a vector, you
can refer to most "robotics" texts, also texts for "computer graphics".

A good book is "Mathematical Elements for Computer Graphics" by Rogers
and Adams (McGraw Hill, 1976) but most have this sort of thing in. A'
another book is Introduction to computing with geometry by Bowyer and
Woodwark (Information Geometers, 1993).

Hope this helps


Mark


#############################
From:     Dr Malcolm E Parker
#############################

Hi
   If T0 and T1 are the original and final 3*3 co-ordinate matrices and R is
your transformation (in this case rotation) matrix then it is the following
least squares calculation is required:-

   if T0 * R = T1

 then      R = (T0t * T0)**-1 * T0t * T1

 where T0t is the transpose of T0. The inverse of the covariance matrix can be
calculated via NAG routine or probably numerical recipes. Good luck.

--

Dr Malcolm Parker               | email: m.e.parker@surrey.ac.uk
Department of Chemistry,        | www:   http://www.chem.surrey.ac.uk/~chs1mp
University of Surrey,           |
Guildford, Surrey. GU2 5XH. UK. | Tel: (01483) 300800x2580  Fax: (01483) 259514
                                |(International calls replace 01483 by +44 1483)

#######################
From:     Konrad Hinsen
#######################


First of all, there is no unique answer. There are infinitely many
combinations of rotation and translation that will do the job. The
rotations differ in the point around which you rotate, but not in
axis and amount.

A convenient choice is to define the translation by the difference
between the centers of mass (if you have no masses, take the centre of
volume). Then the rotation will be around an axis passing through this
centre of mass. All three displacement vectors must be perpendicular
to this axis, and that is sufficient information to find its direction
(Take the cross product of two non-equal displacement vectors. If all
three are equal, then your three points are on a line which is
parallel to the axis). After that, finding the angle of rotation
is a simple trigonometric problem, which however I will not attempt
to solve this late in the day...
--
-------------------------------------------------------------------------------
Konrad Hinsen                          | E-Mail: hinsen@ibs.ibs.fr
Laboratoire de Dynamique Moleculaire   | Tel.: +33-76.88.99.28
Institut de Biologie Structurale       | Fax:  +33-76.88.54.94
41, av. des Martyrs                    | Deutsch/Esperanto/English/
38027 Grenoble Cedex 1, France         | Nederlands/Francais
-------------------------------------------------------------------------------
##########################
From:    David Heisterberg
##########################


Look on the ccl archives for fitest (Fortran) or quaternion-fit (C).
Of course for three points this method probably isn't optimal, but
it's very robust and will give you essentially the exact rotation
matrix.  If you do want the best way, that's pretty easy.  Just
translate T1 so that the centroid is the same as for T0, rotate
T1 so that the P1s are coincident, then rotate about P1 to match
up P2 and P3.  For the initial rotation to match P1, find the
cross product of P1 in the initial and final configuration and
use that as the axis of rotation.

Dave Heisterberg


>>>>>>>>>>>>Alfonso Pozzan Ph.D, GlaxoWellcome
e-mail: ap16390@ggr.co.uk, fax: +39-45-9218196
via Fleming 2, 37100 Verona ITALY <<<<<<<<<<<<

From Schiffer@MSMWIA.hoechst.hoechst-ag.d400.de  Thu Oct 24 06:31:49 1996
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From: "Schiffer, Heinz, Dr., WIA / SC" <Schiffer@MSMWIA.hoechst.hoechst-ag.d400.de>
Message-ID:  <004DAC30.MAI*/S=Schiffer/OU=MSMWIA/O=HOECHST/PRMD=hoechst-ag/ADMD=dbp/C=de/@MHS>
To: CCL <chemistry@www.ccl.net> (Receipt Notification Requested) (Non Receipt Notification Requested)
Subject:  Charges



Hi all,
>from time to time there is a discussion about the construction and the use
of point
charges in molecules. I think there is no doubt within the community, that 
for
intermolecular interactions one should use charges ( and point dipoles, 
point
quadrupoles, etc ) which are adjusted to reproduce as good as possible the
electrostatic potential of the molecule. For qualitative discussions of 
chemical
bonding the use of various population analysis ( Mulliken; 
Davidson-Roby-Ahlrichs,
natural orbital populations of  Weinhold; Bader; etc. By the way : There is
a very promising new one of Marco Haeser in JACS, Vol. 118, 1996, pp. 
7311-7325,
which I think is more rigorous as any previous ones and without any ad hoc
postulates.) are most appropriate.  The fitting of the electrostatic 
potential of a
molecule is a highly non-trivial subject ( see e.g. Michelle Miller Francl 
et al.,
J. Comput. Chem., Vol. 17, 1996, pp. 367-383, and the very recent review by
Sarah L. Price, J. Chem. Soc., Faraday Trans., Vol. 92, 1996, pp. 2997-3008 
)
and in my view not a really solved problem, especially for large molecules.
Now I became aware of a series of papers by George G. Hall and his coworkers
about the fitting of electron densities, which I never heart off bevor and 
which, I think,
are quite unknown to the community. Hall et al. fit the calculated electron 
densities
of molecules to atom-centered gaussians as it is done by many DFT-programs
( "density fitting with an auxillary basis" ) and got a very good ( in my 
view an
excellent ) representation of the electrostatic potential of a molecule. 
Those DFT-
programs with charge density fitting are able to calculate the charge 
density of
molecules  within density functional theory with more than thousand basis 
functions
on a single workstation in about an hour of cpu-time ( see e.g. Karin 
Eichkorn et al.,
Chem. Phys. Lett. 240 (1995) 283-290 ). As a by-product of the calculation 
one gets
an excellent fit of the electrostatic potential of the molecule with 
gaussians. After some
minor modifications of the programs one gets from this point charges, point 
dipoles,
point quadrupoles, etc. or if one likes it the current bun model of Hall and 
coworkes.
My question to the community is now, wether anyone else has similar thoughts 
or
even experiences with this sort of density fitted electrostatic potentials ?
Does anyone has an opinion about using such charge models in force field
calculations ( energy minimization of molecular crystals or molecular 
dynamics
calculation of fluids ) ? Please send responses to the list, so that anyone 
else can
follow the discussion.
Ciao,
Heinz

PS: Here are the references of Hall and coworkers :

     George G. Hall and David Martin
     Approximate Electron Densities for Atoms and Molecules
     Isr. J. Chem. 19 (1980) 255-259

     G. G. Hall and C. M. Smith
     Fitting Eelectron Densities of Molecules
     Int. J. Quantum Chem. 25 (1984) 881-890

     G. G. Hall and K. Tsujinaga
     The molecular electrostatic potential of some simple molecules
     Theor. Chim. Acta 69 (1986) 425-436

     K. Tsujinaga and G. G. Hall
     The currant bun model of simple molecules
     Theor. Chim. Acta 70 (1986) 257-264

 ----------------------------------------------------------------------------  
 -----------------------------------------------
Dr. Heinz Schiffer            65926 Frankfurt am Main
Hoechst AG               Phone ++49-69-305-2330
Scientific Computing          Fax   ++49-69-305-81162

Email :   schiffer@wia.hoechst-ag.d400.de
     schiffer@msmwia.hoechst.hoechst-ag.d400.de
 ----------------------------------------------------------------------------  
 ----------------------------------------------- 

From melchers@chemie.fu-berlin.de  Thu Oct 24 08:31:44 1996
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From: melchers@chemie.fu-berlin.de (Bernd Melchers)
Subject: Charmm24-benchmark PPro versus SGI
To: chemistry@www.ccl.net
Date: Thu, 24 Oct 1996 14:02:28 +0200 (MEST)
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hello,
we performed some charmm24 benchmarks with a Pentium Pro and with some
Silicon Graphics machines:

1. modelling (select, coor orien, hbuild) and some energy minimization
(i.e. integer and floating point)
a) R4600 100 MHz     24.45 MINUTES
b) R4400 150 MHz     14.08 MINUTES
c) R8000  75 MHz      7.21 MINUTES
d) PPro  200 MHz      5.53 MINUTES
e) R10000 195MHz      2.51 MINUTES


2. molecular dynamik simulation (i.e. much floating point)
f) R4000 100 MHz   4.36 hours
b) R4400 150 MHz   2.90 hours
d) PPro  200 MHz   1.29 hours


machine/compiler description:

a) Indy, IRIX-5.3, R4600SC, 100 MHz, 16+16/0 Cache, cc -O2
b) Indigo, IRIX-5.3, R4400, 150 MHz, 16+16/1024 Cache, cc -O2
c) Power Indigo^2, IRIX-6.2, R8000, 75 MHz, 16+16/2048 Cache, cc -O3 -mips4
d) PentiumPro Asus Natoma Board, 200 MHz, 16+16(?)/256 Cache, gcc-2.7.2/
   g77-0.5.18 -O2 running linux kernel 2.0.18
e) R10000, IRIX-6.2, 195 MHz, 32+32/1024 Cache, cc -O3 -mips4
f) Indigo R4000, IRIX-5.3, 100 MHz, 16+16/1024 Cache, cc -O2

the results are not too bad for the intel chips, aren't they?

Ciao
Bernd
-- 
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-+-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Bernd Melchers                   | melchers@FU-Berlin.DE
Freie Universitaet Berlin        |
Institut fuer Kristallographie   | Please replace battery pack,
Takustr. 6                       | attach external power,
D 14195 Berlin                   | or system will be
Germany                          | shutdown in 10 seconds.
Earth                            |
Tel.: ++49-30-8383612            | Fax.: ++49-30-8383464
picture and pgp key: http://www.chemie.fu-berlin.de/~melchers
                 "We don't write software, we compose it."
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-+-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

From hinsen@ibs.ibs.fr  Thu Oct 24 09:31:46 1996
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Date: Thu, 24 Oct 96 14:36:36 +0100
From: Konrad Hinsen <hinsen@ibs.ibs.fr>
To: Schiffer@MSMWIA.hoechst.hoechst-ag.d400.de
Cc: chemistry@www.ccl.net
In-Reply-To: 
	<004DAC30.MAI*/S=Schiffer/OU=MSMWIA/O=HOECHST/PRMD=hoechst-ag/ADMD=dbp/C=de/@MHS>
Subject: Re: CCL:G:Charges


> postulates.) are most appropriate.  The fitting of the electrostatic 
> potential of a
> molecule is a highly non-trivial subject ( see e.g. Michelle Miller Francl 
> et al.,
> J. Comput. Chem., Vol. 17, 1996, pp. 367-383, and the very recent review by
> Sarah L. Price, J. Chem. Soc., Faraday Trans., Vol. 92, 1996, pp. 2997-3008 
> )
> and in my view not a really solved problem, especially for large molecules.

I don't agree. The charge fitting problem is not essentially different
>from other fitting problems in all branches of science and
engineering, and lots of articles and books have been written about
it. There are well established and robust techniques to find optimal
charges and to judge to what degree they are well determined by the
reference data. Much of this is not generally known in the computational
chemistry community, but that's another problem.

There remains of course the problem that the electrostatic potential
in a reasonable region may not be sufficient to determine all charges
uniquely. But that is not really fatal: if after adding all reference
data you can reasonably get (e.g. from multiple conigurations) some
charges still remain illdetermined, then they probably don't matter
much in real life. If they do, then probably the fixed point charge model
is not good enough.

> are quite unknown to the community. Hall et al. fit the calculated electron 
> densities
> of molecules to atom-centered gaussians as it is done by many DFT-programs
> ( "density fitting with an auxillary basis" ) and got a very good ( in my 
> view an
> excellent ) representation of the electrostatic potential of a molecule. 

Essentially that means choosing a more complicated model (gaussian densities
rather than point charges), and it is not surprising that you can get
better results. The question is whether people are willing to work with
such more complicated models in their force fields. It is certainly
worthwhile exploring in which situations such models can give better
results.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                          | E-Mail: hinsen@ibs.ibs.fr
Laboratoire de Dynamique Moleculaire   | Tel.: +33-76.88.99.28
Institut de Biologie Structurale       | Fax:  +33-76.88.54.94
41, av. des Martyrs                    | Deutsch/Esperanto/English/
38027 Grenoble Cedex 1, France         | Nederlands/Francais
-------------------------------------------------------------------------------

From chpajt@bath.ac.uk  Thu Oct 24 10:31:44 1996
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          by goggins.bath.ac.uk with SMTP (PP); Thu, 24 Oct 1996 15:10:26 +0100
Date: Thu, 24 Oct 1996 15:10:02 +0100 (BST)
From: A J Turner <chpajt@bath.ac.uk>
To: "Schiffer, Heinz, Dr., WIA / SC" <Schiffer@msmwia.hoechst.hoechst-ag.d400.de>
cc: CCL <chemistry@www.ccl.net>
Subject: Re: CCL:G:Charges
In-Reply-To: <004DAC30.MAI*/S=Schiffer/OU=MSMWIA/O=HOECHST/PRMD=hoechst-ag/ADMD=dbp/C=de/@MHS>
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Hi!

I am working on the charge fitting area right now.  My experiance may be
of interest.  The approxiation of placing charges on nuclear centres can
greatly outweigh to variation in method of attaining the charges in the
first place.

I am using QM/MM technology to _directly_ fit a MM force field to a QM/MM
force field.  This shows that several 'off centre' points _must_
be included if one is to get anything like a reasonable fit of the mm
forces to the qm ones.  My present example being ch3o- , where the forcing
of the negative charg onto the 'centre' of the oxygen causes maiisve
'artificial' +ve charge build up on the carbon and hence large negaive
charges on the protons.  The use of a QM/MM force field where the same vdw
paramters apply shows that these negative protons are very very far from
correct.

Does anyon else have similar experiances?

Best wishes

Alex

 -------------------------------------------------------------------
|Alexander J Turner         |A.J.Turner@bath.ac.uk                  |
|Post Graduate              |http://www.bath.ac.uk/~chpajt/home.html|
|School of Chemistry        |+144 1225 8262826 ext 5137             |
|University of Bath         |                                       |
|Bath, Avon, U.K.           |Field: QM/MM modeling                  |
 ------------------------------------------------------------------- 



From kotelyan@che.udel.edu  Thu Oct 24 15:31:47 1996
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Date: Thu, 24 Oct 1996 14:31:37 +22305133 (EDT)
From: Michael Kotelyanskii <kotelyan@che.udel.edu>
Subject: Re: CCL:Charmm24-benchmark PPro versus SGI
To: Bernd Melchers <melchers@chemie.fu-berlin.de>
Cc: chemistry@www.ccl.net
In-Reply-To: <m0vGOUX-008pubC@Bose.Chemie.FU-Berlin.DE>
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That's interesting ,
but why is R10000 missing from the MD ?

Michael Kotelyanskii PhD
Department of Chemical Engineering
University of Delaware                          kotelyan@che.udel.edu
Newark DE 19716                                    


On Thu, 24 Oct 1996, Bernd Melchers wrote:

> hello,
> we performed some charmm24 benchmarks with a Pentium Pro and with some
> Silicon Graphics machines:
> 
> 1. modelling (select, coor orien, hbuild) and some energy minimization
> (i.e. integer and floating point)
> a) R4600 100 MHz     24.45 MINUTES
> b) R4400 150 MHz     14.08 MINUTES
> c) R8000  75 MHz      7.21 MINUTES
> d) PPro  200 MHz      5.53 MINUTES
> e) R10000 195MHz      2.51 MINUTES
> 
> 
> 2. molecular dynamik simulation (i.e. much floating point)
> f) R4000 100 MHz   4.36 hours
> b) R4400 150 MHz   2.90 hours
> d) PPro  200 MHz   1.29 hours
> 
> 
> machine/compiler description:
> 
> a) Indy, IRIX-5.3, R4600SC, 100 MHz, 16+16/0 Cache, cc -O2
> b) Indigo, IRIX-5.3, R4400, 150 MHz, 16+16/1024 Cache, cc -O2
> c) Power Indigo^2, IRIX-6.2, R8000, 75 MHz, 16+16/2048 Cache, cc -O3 -mips4
> d) PentiumPro Asus Natoma Board, 200 MHz, 16+16(?)/256 Cache, gcc-2.7.2/
>    g77-0.5.18 -O2 running linux kernel 2.0.18
> e) R10000, IRIX-6.2, 195 MHz, 32+32/1024 Cache, cc -O3 -mips4
> f) Indigo R4000, IRIX-5.3, 100 MHz, 16+16/1024 Cache, cc -O2
> 
> the results are not too bad for the intel chips, aren't they?
> 
> Ciao
> Bernd
> -- 
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-+-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> Bernd Melchers                   | melchers@FU-Berlin.DE
> Freie Universitaet Berlin        |
> Institut fuer Kristallographie   | Please replace battery pack,
> Takustr. 6                       | attach external power,
> D 14195 Berlin                   | or system will be
> Germany                          | shutdown in 10 seconds.
> Earth                            |
> Tel.: ++49-30-8383612            | Fax.: ++49-30-8383464
> picture and pgp key: http://www.chemie.fu-berlin.de/~melchers
>                  "We don't write software, we compose it."
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