From chuang@iris.bc.ntu.edu.tw  Thu Mar 23 01:22:38 1995
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Date: Thu, 23 Mar 95 14:15:24 -0800
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To: DIBUG@comp.bioz.unibas.ch
Subject: correlation time estimation
Cc: amber@cgl.ucsf.EDU, quanta-l@msi.com, xplor-l@msi.com, str-nmr@net.bio.net,
        chemistry@ccl.net, molmodel@net.bio.net



Dear netters: 

When doing NOE simulation from structure, it is needed to give the correlation time value. Yah, to my know, it is dependent on the molecular weight, the shape
(structure) of the molecule. How to roughtly estimate the correlation time when doing this kind of calculation ???

Any suggestion will be great appreciated.

Any suggestion can mail to me directly. Thanks.

ccchuang

  ============================================================
    Chyh-Chong Chuang
    Institude of Biological Chemistry, 
    Academia Sinica,Taipei, Taiwan
  ------------------------------------------------------------
    P.O. BOX 23-106,      Phone: (02) 362-0261 ext 2021
    Taipei, Taiwan,       Fax: (02) 363-5038
    R.O.C.                E-Mail: chuang@bc.ntu.edu.tw
  ============================================================


From gl@coil.mdy.univie.ac.at  Thu Mar 23 05:37:42 1995
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From: "Gerald Loeffler" <gl@coil.mdy.univie.ac.at>
Message-Id: <9503231133.ZM2457@coil.mdy.univie.ac.at>
Date: Thu, 23 Mar 1995 11:33:52 +0100
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Hi!

Do you know of a mailing list or newsgroup dedicated to Axel Bruengers X-PLOR ?

	Thank you

(hope this isn't a FAQ)
--
Gerald Loeffler
PhD student in Theoretical Biochemistry

Email: gl@mdy.univie.ac.at
Phone: +43 1 40480 612
Fax:   +43 1 4028525
Mail:  University of Vienna
       Institute for Theoretical Chemistry
       Theoretical Biochemistry Group
       Waehringerstrasse 17/Parterre
       A-1090 Wien, Austria

#include "fancy_ASCII_picture"
#include "funny_statement"
#include "standard_disclaimer"



From qftramos@usc.es  Thu Mar 23 07:07:45 1995
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Date: Thu, 23 Mar 1995 12:59:29 +0100
From: qftramos@usc.es (Antonio Fernandez Ramos)
Message-Id: <199503231159.AA01839@uscmail.usc.es>
To: chemistry@ccl.net
Subject: least squares fit


  Dear netters,
I am trying to do a non linear least squares fit, 
using a Marquardt type algoritm, but I need to restrict some
parameters to make my function behaves correctly.
Is available any program to constrain parameters to be positive?

Thanks.



From tevelde@chem.vu.nl  Thu Mar 23 07:37:43 1995
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To: CHEMISTRY@ccl.net
From: tevelde@chem.vu.nl (Bert te Velde)
Subject: optimization with constraints


Dear Antonio (CCL),

>I am trying to do a non linear least squares fit,
>using a Marquardt type algoritm, but I need to restrict some
>parameters to make my function behaves correctly.
>Is available any program to constrain parameters to be positive?

formulate your problem with transformed parameters, such that
p_new = ln(p_old)
optimize p_new (without constraints) and obtain your original parameter (p_old) as
p_old = exp(p_new)

(this is just one of the many transformations that map {-inf,+inf} onto {0,+inf}.
Any other transformation that does the same might be used equally well. Sometimes the nature of the problem suggests a particular transformation.
The choice of transformation may affect the efficiency of the optimization algorithm)

bye

------------------------------------------------------------------------
Bert te Velde                       SCIENTIFIC COMPUTING & MODELLING
phone:  +31-20 44 47625 (direct)    Vrije Universiteit, Theor. Chemistry
                  47644 (secr.)     De Boelelaan 1083
fax     +31-20-44 47643             1081 HV Amsterdam
e-mail: tevelde@chem.vu.nl          The Netherlands
------------------------------------------------------------------------



From Matthew.Harbowy@tjlus.sprint.com  Thu Mar 23 09:52:46 1995
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To: chemistry@ccl.net
Subject:  BSSE and semiempirical methods


     One of the drawbacks of doing 'corrections', no matter how valid or 
     seemingly necessary, on semiempirical methods such as AM1, is that the 
     parameterization is fitted such that energies and geometries are
     'corrected' to compensate for the limitations of the method.
     
     This means that, if you would like to do CI, or BSSE removal, or amy 
     other 'very appropriate' 'improvement' technique, you are, in some 
     sense, double-correcting. What that means for transition states and 
     reactive intermediates is anyone's guess: however, doing limited CI to 
     'correct' the wavefunction to non-closed-shell states seems ok, but 
     doing extensive CI to get 'accurate' energies seems pointless.
     
     But, it would seem that BSSE should be present in semiempirical 
     methods.
     
     matthew e. harbowy
     thomas j. lipton, inc.

From raman@bioc01.uthscsa.edu  Thu Mar 23 10:07:48 1995
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From: raman@bioc01.uthscsa.edu (C.S.RAMAN)
Message-Id: <9503231500.AA11848@bioc01.uthscsa.edu>
Subject: Re: CCL:? X-PLOR mailing list/newsgroup ?
To: gl@coil.mdy.univie.ac.at (Gerald Loeffler)
Date: Thu, 23 Mar 1995 09:00:38 -0600 (CST)
Cc: chemistry@ccl.net
In-Reply-To: <9503231133.ZM2457@coil.mdy.univie.ac.at> from "Gerald Loeffler" at Mar 23, 95 11:33:52 am
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> Do you know of a mailing list or newsgroup dedicated to Axel Bruengers X-PLOR ?

Try xplor-l@msi.com  (sending messages to this address will be
distributed to the entire list).

Cheers
-raman
-- 
   _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
   _/                                                                      _/
   _/                           C.S.RAMAN                                  _/
   _/                   Department of Biochemistry                         _/
   _/            University of Texas Health Science Center                 _/
   _/                     7703 Floyd Curl Drive                            _/
   _/                  San Antonio, TX 78284-7760                          _/
   _/                              USA                                     _/
   _/                                                                      _/
   _/                    Tel:     (210) 567-6623                           _/
   _/                    Fax:     (210) 567-6595                           _/
   _/                 E-mail:  raman@bioc01.uthscsa.edu                    _/
   _/                                                                      _/
   _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/  
   _/                                                                      _/
   _/      How can it be that mathematics, a product of human thought      _/ 
   _/      independent of experience, is so admirably adapted to the       _/ 
   _/      objects of reality?   "-Albert Einstein"                        _/
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From gavin@vangogh.chem.uab.edu  Thu Mar 23 11:07:47 1995
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To: CHEMISTRY@ccl.net
Subject: bond order analysis



   Dear Netters,

        What commerical programs can do the ab initio calculations
  of the bond order ? ANY INFO will be appreciated !


                                    Gavin
                              gavin@vangogh.chem.uab.edu


From WSMITH@msnet.mathstat.uoguelph.ca  Thu Mar 23 11:07:50 1995
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Organization:  Dept. of Math & Stats.
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Date:          Thu, 23 Mar 1995 11:01:32 EDT
Subject:       Re: CCL:least squares fit
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Hi,

    There are many ways (and there is more to it than just this) but 
the simplest way to get what you want is to just replace your 
parameter a by another parameter a^2 in your model.

    BTW, Marquardt-type algorithms are _bound_ to fail to converge 
in many cases - so beware.  The best is to use a _real_ nonlinear 
optimization code.


>  Dear netters,
>I am trying to do a non linear least squares fit, 
>using a Marquardt type algoritm, but I need to restrict some
>parameters to make my function behaves correctly.
>Is available any program to constrain parameters to be positive?
>

Best Regards,


W. R. Smith                        Professor
                                   Dept. of Mathematics and Statistics
                                   and School of Engineering 
                                   University of Guelph
FAX: 519-837-0221                  Guelph, Ontario
Tel: 519-824-4120, ext. 3038       CANADA N1G 2W1

From hans.lischka@itc.univie.ac.at  Thu Mar 23 11:14:20 1995
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From: hans.lischka@itc.univie.ac.at (Hans Lischka)
Message-Id: <199503231603.AA21263@retsina.itc.univie.ac.at.>
Subject: MRCI, COLUMBUS query
To: chemistry@ccl.net
Date: Thu, 23 Mar 1995 17:03:22 +0100 (MEZ)
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Dear Netters,

since there have been some enquiries on the COLUMBUS program recently I 
would like to take this opportunity to inform interested people about
an extended version of COLUMBUS which is available on our anonymous ftp server
ftp.itc.univie.ac.at in Vienna. Look into the directory pub/quant/COLUMBUS
for columbus.new.date.tar.Z (where date stands for a date which is updated
from time to time).

The procedures for installation are very similar to the original ones (for
details see the README.NEW file). Some of the new features are:

availability of the analytical MRCI gradient
interactive input routines (they make life much easier now!)
geometry optimization routines
first-order properties
polarizabilities via finite field calculation
ACPF and MR-AQCC methods

and for those who are interested to get experience with parallel computing
we have a parallel version of the CI section of the program. It
works very well on about 100 processors of the Intel-Paragon (depending on the
size of the CI problem which was 4 million in our case), it is being tested
on the IBM SP1/SP2 and also works on workstation clusters.
Porting to other parallel platforms should not be too difficult as long
as the global array tools developed by Robert Harrison (PNL) are available.

One has to note that the new features are not as well tested yet as those of
the original program! For comments or questions please contact me (address
see below) or Ron Shepard at shepard@tcg.anl.gov.

Hans

Hans Lischka
Institute for Theoretical Chemistry and Radiation Chemistry
University of Vienna, Austria
e-mail: lischka@itc.univie.ac.at 

From elewars@alchemy.chem.utoronto.ca  Thu Mar 23 11:52:50 1995
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From: "E. Lewars" <elewars@alchemy.chem.utoronto.ca>
Message-Id: <199503231643.LAA23359@alchemy.chem.utoronto.ca>
To: chemistry@ccl.net
Subject: PYRROLE Z-MATRIX


Daniel Glossman said he lost the pyrrole Z-matrix suggestions and asked for
a re-mailing of them.  I lost his email address so I have to send my response
to the net again.
The internal coord's of atoms in cyclic systems shouldn't be defined
sequentially, because of the ratcheting effect (Tim Clark, *A Handbook of
Computational Chemistry*).  Labelling distances X2N1..., angles A432..., and
dihedrals D4321.... will make Z-matrices easier to interpret, till the happy
day when they are extinct and everyone uses Cartesians and an interactive
model-builder.
The input param's are from a MM opt with the Sybil forcefield, using Spartan
for visualization.

===========

# etc etc [for a Gaussian job]

PYRROLE, C2V

0 1
N1
X2       N1    X2N1
C3       X2    C3X2      N1    90.
C4       C3    C4C3      X2    A432    N1      0.
C5       X2    C3X2      N1    90.     C3    180.
C6       C5    C4C3      X2    A432    N1      0.
H7       C6    H7C6      C5    A765    X2    180.
H8       C5    H8C5      C6    A856    X2    180.
H9       C3    H8C5      C4    A856    X2    180.
H10      C4    H7C6      C3    A765    X2    180.
H11      X2    H11X2     C3    90.     C4      0.

        X2N1         1.9970
        C3X2         0.7345
        C4C3         1.3351
        H7C6         1.090
        H8C5         1.089                               z
        A432       105.5                               /\
        A765       125.8                 H9            |            H8
        A856       127.5                   \           |          /
        H11X2        3.029                   \         |        /
                                               C3------X2-----C5
                                              /        |        \
                                  H10--- C4 /          |          \C6 ---H7
                                                       |
                                                       |
                            x < ----------------------N1
                                                      /|
                                                     / |
                                                   /   H11
                                                 y



From mjf@iris120.biosym.com  Thu Mar 23 12:26:45 1995
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From: mjf@biosym.com (Mark J Forster )
Message-Id: <199503231717.JAA14325@iris120.biosym.com>
To: chuang@bc.ntu.edu.tw
Subject: Correlation time estimation
Cc: chemistry@ccl.net



Dear Chyh-Chong

The most accurate method of correlation time estimation would be 
measurement of (say) 13C or 15N relaxation for a nucleus with
a directly attached proton and with out extensive molecular motion,
so a backbone 15N in a protein would be suitable. An H-H noe build
up rate between say a Gly HA1-HA2 might also be suitable. In
DNA the Cyt H5-H6 vector is of fixed length and is often used 
for this purpose.

If you want a very rough method, that my experience suggests is
still within a factor of two, the try 
	MW in KDa = tauc_c in ns
of true tau_c values depend upon the temperature, solvent etc
and can in practice differ for different atom-atom vectors in the
molecule if it exhibits differential mobility.

There are also formulas based upon hydrodynamic models in the 
literature that can predict tau_c for both isotropic and anisotropic
reorientation. 

Hope this helps.

From momot@iris5.chem.Arizona.EDU  Thu Mar 23 14:22:49 1995
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Date: Thu, 23 Mar 1995 12:19:06 -0700 (MST)
From: Konstantin Momot <momot@iris5.chem.Arizona.EDU>
Subject: Re: correlation time estimation
In-reply-to: <01HOGZ4WTO6A9852DT@Arizona.EDU>
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On Wed, 22 Mar 1995 chuang@iris.bc.ntu.edu.tw wrote:

> Dear netters: 
> 
> When doing NOE simulation from structure, it is needed to give the correlation time value. Yah, to my know, it is dependent on the molecular weight, the shape
> (structure) of the molecule. How to roughtly estimate the correlation time when doing this kind of calculation ???
> 
> Any suggestion will be great appreciated.
> 
> Any suggestion can mail to me directly. Thanks.
> 
> ccchuang
> 

In general, this depends on the particular model of molecular motion
you assume. The most consistent discussion of the question is given in
Abragam's book, Ch.VIII, Part E (especially pp. 298-300 of the last
English edition). 

If you only consider rotation in a liquid and assume the molecule to be a
rigid sphere (very rough estimate, but sufficient for most practical
problems !), then you have the correlation time

          4pi*R^3*mu/3kT

where mu is solvent's viscosity and R is the molecule's radius.

Cheers,

Konstantin             <momot@iris5.chem.arizona.edu>





From separk@cs.usc.edu  Thu Mar 23 20:52:54 1995
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Date: Thu, 23 Mar 95 17:49:09 PST
From: SEONGBIN PARK <separk@cs.usc.edu>
To: CHEMISTRY@ccl.net
Subject: elementary question (rms deviation)
Message-ID: <CMM.0.90.2.796009749.separk@pollux.usc.edu>


Hello,

I am sure this is a very elementary question, but simply I do not know
the answer and hope someone else knows the answer.
My question is : 

      Why is "standard deviation" called "rms deviation" ?

I think they are exactly same.  However, only "rms deviation" seems
to be used in the molecular structure comparison literature.

Thank you very much for your time !

Regards,
Seongbin Park (separk@pollux.usc.edu)

From chiremv!andromeda!martine@uunet.uu.net Thu Mar 23 16:20:56 1995
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From: chiremv!andromeda!martine@uunet.uu.net (Eric Martin)
Message-Id: <9503232048.AA07252@andromeda>
To: uunet!ccl.net!chemistry@uunet.uu.net
Subject: Re:  CCL:optimization with constraints



Dear Antonio & Bert (CCL),

>>I am trying to do a non linear least squares fit,
>>using a Marquardt type algoritm, but I need to restrict some
>>parameters to make my function behaves correctly.
>>Is available any program to constrain parameters to be positive?
> 
> formulate your problem with transformed parameters, such that
> p_new = ln(p_old)
> optimize p_new (without constraints) and obtain your original parameter (p_old) as
> p_old = exp(p_new)
> 
> (this is just one of the many transformations that map {-inf,+inf}
> onto {0,+inf}.  Any other transformation that does the same might be
> used equally well. Sometimes the nature of the problem suggests a
> particular transformation.  The choice of transformation may affect the
> efficiency of the optimization algorithm) 

My understanding is that fitting a transformed function might not only
affect the efficiency, it can also affect the answer.  The least
squares best fit of the transformed problem will have different
parameter values (even after the reverse transorm) than the best fit of
the untransformed (albeit constrained) problem, since the sum of
squared residuals of a different function is being minimized.  This can
sometimes be rectified by applying weighted least squares.  See:
"When, Why and How to Use Weighted Least Squares", Robert de Levie, J.
Chem. Edu., 63, (1986) p. 10.

Best,  -Eric

Eric Martin
martine@chiron.com
4560 Horton St., Emeryville, CA 94608
(510)601-3306,  FAX (510)601-3360



