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Date: Fri, 8 Aug 2003 08:20:37 +0200
Subject: Re: CCL:summary for program for superimposing (small) molecules and new  question
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From: Marcel Swart <swart~at~chem.vu.nl>
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Supposing that the RMSD as calculated by QMol is smaller, QMol does it=20=

more smartly
than the crude Excel way. Of course, when slightly translating one of=20
the molecules,
in combination with a slight rotation might lower the RMSD.

I have written a small F90 program that does just this, first get all=20
coords relative
to the center of masses, and then rotate one of the molecules in order=20=

to find the "optimum"
rotation for the RMSD to be lowest.

I suppose this is exactly what QMol does also.

On Thursday, Aug 7, 2003, at 21:57 Europe/Amsterdam, Dr. Richard L.=20
Wood wrote:

> I have a question as to how the program QMol calculates the RMSD of=20
> two structures.
>
> I used Excel to calculate the RMSD for two different conformations of=20=

> the same molecule and compared the result that I get using QMol, and I=20=

> get two different values, and I am wondering why that is.
>
> In Excel, I calculated the distances between the same two atoms in the=20=

> two conformations, squared them, added them up, then divided by the=20
> number of atoms.
> After this, take the square root to get the RMSD.
>
> It looks to me like QMol does something different.
>
> Thanks in advance,
> Richard
> =A0
>
> =46rom Jason D. Gans:=A0Hello,
>
> Qmol, available from the CCL software repository
>
> http://www.ccl.net/cca/software/MS-WIN95-NT/qmol/index.shtml
>
> can superimpose molecules and compute RMS deviation.
>
> Regards,
>
> Jason Gans
>
> B division
> Los Alamos National Lab=A0
>
>
> --
> Richard L. Wood, Ph. D.
> Physical/Computational Chemist
> =A0
> =A0
>
>
=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=
=96=96=96=96=96=96=96=96=96=96=96=96
dr. Marcel Swart

Organische en Anorganische Chemie
Faculteit der Exacte Wetenschappen
Vrije Universiteit Amsterdam

De Boelelaan 1083
1081 HV Amsterdam
The Netherlands

F   +31-(0)20-4447488
E   swart~at~chem.vu.nl
W  http://go.to/m.swart
=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=
=96=96=96=96=96=96=96=96=96=96=96=96

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Supposing that the RMSD as calculated by QMol is smaller, QMol does it
more smartly

than the crude Excel way. Of course, when slightly translating one of
the molecules,

in combination with a slight rotation might lower the RMSD.


I have written a small F90 program that does just this, first get all
coords relative

to the center of masses, and then rotate one of the molecules in order
to find the "optimum"

rotation for the RMSD to be lowest.


I suppose this is exactly what QMol does also.


On Thursday, Aug 7, 2003, at 21:57 Europe/Amsterdam, Dr. Richard L.
Wood wrote:


<excerpt>I have a question as to how the program QMol calculates the
RMSD of two structures.


I used Excel to calculate the RMSD for two different conformations of
the same molecule and compared the result that I get using QMol, and I
get two different values, and I am wondering why that is.


In Excel, I calculated the distances between the same two atoms in the
two conformations, squared them, added them up, then divided by the
number of atoms.

After this, take the square root to get the RMSD.


It looks to me like QMol does something different.


Thanks in advance,

Richard

=A0


<fontfamily><param>Arial</param><smaller>=46rom Jason D.
=
Gans:</smaller></fontfamily>=A0<fontfamily><param>Arial</param>Hello,</fon=
tfamily>


<fontfamily><param>Arial</param>Qmol, available from the CCL software
repository</fontfamily>


=
<underline><fontfamily><param>Arial</param><color><param>1999,1999,FFFF</p=
aram>http://www.ccl.net/cca/software/MS-WIN95-NT/qmol/index.shtml</color><=
/fontfamily></underline>


<fontfamily><param>Arial</param>can superimpose molecules and compute
RMS deviation.</fontfamily>


<fontfamily><param>Arial</param>Regards,</fontfamily>


<fontfamily><param>Arial</param>Jason Gans</fontfamily>


<fontfamily><param>Arial</param>B division

Los Alamos National Lab</fontfamily>=A0



--

Richard L. Wood, Ph. D.

Physical/Computational Chemist

=A0

=A0



=
</excerpt><fontfamily><param>Helvetica</param>=96=96=96=96=96=96=96=96=96=96=
=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=
=96=96

<bold>dr. Marcel Swart

</bold>

Organische en Anorganische Chemie

Faculteit der Exacte Wetenschappen

Vrije Universiteit Amsterdam


De Boelelaan 1083

1081 HV Amsterdam

The Netherlands


F   +31-(0)20-4447488

E   swart~at~chem.vu.nl

W  http://go.to/m.swart

=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=
=96=96=96=96=96=96=96=96=96=96=96=96</fontfamily>


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From chemistry-request@ccl.net Fri Aug  8 06:40:39 2003
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Date: Fri, 8 Aug 2003 12:41:00 +0200
To: "Dr. Daniel Glossman-Mitnik" <daniel.glossman~at~cimav.edu.mx>
From: Per-Ola Norrby <pon~at~kemi.dtu.dk>
Subject: Re: CCL:summary for program for superimposing (small) molecules
 and new question
Cc: <chemistry~at~ccl.net>
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	Dear Daniel,

>Before I present the summary, I was to ask the (neccessary)
>follow-up question:  In your experience, when a comparison
>of an experimental molecular structure (i.e. X-rays) and its
>calculated (Gaussian) counterpart is done, which will be the
>treshold RMSD value which can be considered acceptable ?

	The RMSD value is NOT a good measure of quality.  One reason 
is that soft modes (mainly torsions) are easily distorted by crystal 
packing, leading to huge discrepancies if you only look at RMSD.  A 
case in point is biphenyl, where the crystal adopts a planar 
structure becuase it packs better, whereas the gas phase global 
minimum has a torsion angle around 41 degrees.

	You can either use a comparison that is insensitive to these 
discrepancies, or do the calculation in the crystal (requiring QM 
with periodic boundaries, not in Gaussian).  I'd recommend comparison 
of lists of bond lengths and angles.  Alternatively, you can use the 
energy of the crystal structure calculated by Gaussian and compare it 
to the global minimum in Gaussian, but that requires constrained 
relaxation of the crystal structure to allow for differences in 
paradigm between X-ray and QM.

	Best regards,

	Per-Ola Norrby
-- 
Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/
Technical University of Denmark, Department of Chemistry
Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
Email: pon~at~kemi.dtu.dk  tel +45-45252123,  fax +45-45933968
--============_-1151783229==_ma============
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<!doctype html public "-//W3C//DTD W3 HTML//EN">
<html><head><style type="text/css"><!--
blockquote, dl, ul, ol, li { padding-top: 0 ; padding-bottom: 0 }
 --></style><title>Re: CCL:summary for program for superimposing
(small)</title></head><body>
<div><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </x-tab>Dear
Daniel,</div>
<div><br></div>
<blockquote type="cite" cite><font face="Arial" size="-1">Before I
present the summary, I was to ask the (neccessary)</font></blockquote>
<blockquote type="cite" cite><font face="Arial" size="-1">follow-up
question:&nbsp; In your experience, when a
comparison</font></blockquote>
<blockquote type="cite" cite><font face="Arial" size="-1">of an
experimental molecular structure (i.e. X-rays) and
its</font></blockquote>
<blockquote type="cite" cite><font face="Arial" size="-1">calculated
(Gaussian) counterpart is done, which will be the</font></blockquote>
<blockquote type="cite" cite><font face="Arial" size="-1">treshold
RMSD value which can be considered acceptable ?</font></blockquote>
<div><br></div>
<div><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </x-tab>The
RMSD value is NOT a good measure of quality.&nbsp; One reason is that
soft modes (mainly torsions) are easily distorted by crystal packing,
leading to huge discrepancies if you only look at RMSD.&nbsp; A case
in point is biphenyl, where the crystal adopts a planar structure
becuase it packs better, whereas the gas phase global minimum has a
torsion angle around 41 degrees.</div>
<div><br></div>
<div><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </x-tab>You can
either use a comparison that is insensitive to these discrepancies, or
do the calculation in the crystal (requiring QM with periodic
boundaries, not in Gaussian).&nbsp; I'd recommend comparison of lists
of bond lengths and angles.&nbsp; Alternatively, you can use the
energy of the crystal structure calculated by Gaussian and compare it
to the global minimum in Gaussian, but that requires constrained
relaxation of the crystal structure to allow for differences in
paradigm between X-ray and QM.</div>
<div><br></div>
<div><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </x-tab>Best
regards,</div>
<div><br></div>
<div><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </x-tab>Per-Ola
Norrby</div>
<x-sigsep><pre>-- 
</pre></x-sigsep>
<div>Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/<br>
Technical University of Denmark, Department of Chemistry<br>
Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark<br>
Email: pon~at~kemi.dtu.dk&nbsp; tel +45-45252123,&nbsp; fax
+45-45933968</div>
</body>
</html>
--============_-1151783229==_ma============--


From chemistry-request@ccl.net Fri Aug  8 05:30:02 2003
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Subject: Reusing the NAMD code to build C++ simulation program
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Dear CCL'ers,

I am wondering if it is easy to reuse the NAMD code to build C++
simulation program. My question might sound strange because NAMD is so
famous for its high extensibility and object-oriented design with
C++. But NAMD is actually coded in Charm++, an extended C++ for
parallelization, so that the problem is that a programmer has to deal
with Charm++ syntax in the NAMD code and its execution model for
parallel computation.  So, could somebody give me a brief explanation
how the NAMD code can be incorporated into C++ framework, or if it is
possible.

I would appreciate any suggestion or references for a simulation
program which is built by adding C++ code to the NAMD code.

Thanks a lot in advance.

Masakatsu Ito , Ph.D

Grid Technology Research Center
National Institute of Advanced Industrial Science and Technology
Tsukuba Central 2, Tsukuba, Ibaraki 305-8568 Japan
E-mail masakatsu-ito~at~aist.go.jp
URL http://met.sourceforge.net/





From chemistry-request@ccl.net Fri Aug  8 03:51:01 2003
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From: "Mark Mackey" <m.mackey_at_cresset-bmd.com>
To: "'Dr. Richard L. Wood'" <rlw28_at_cornell.edu>
Cc: <chemistry_at_ccl.net>
Subject: RE: summary for program for superimposing (small) molecules and new  question
Date: Fri, 8 Aug 2003 08:50:15 +0100
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Umm, how did you align the two molecules? If you take a molecule and an
exact copy which you translate by 5A, then your Excel method will give
you an RMSD of 5A, which is obviously incorrect.

The standard molecular alignment methods give you the _minimum_ RMSD
i.e. they rigidly rotate and translate the molecules so as to give the
smallest possible RMSD for those two structures. This is the standard
method of determining how 'close' two structures are. Simply calculating
the differences of the input coordinates gives you no useful information
whatsoever.

-- 
Mark Mackey
Cresset Biomolecular Discovery

-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request_at_ccl.net] On
Behalf Of Dr. Richard L. Wood
Sent: 07 August 2003 20:58
To: Dr. Daniel Glossman-Mitnik
Cc: chemistry_at_ccl.net
Subject: CCL:summary for program for superimposing (small) molecules and
new question

I have a question as to how the program QMol calculates the RMSD of two
structures. 
I used Excel to calculate the RMSD for two different conformations of
the same molecule and compared the result that I get using QMol, and I
get two different values, and I am wondering why that is. 
In Excel, I calculated the distances between the same two atoms in the
two conformations, squared them, added them up, then divided by the
number of atoms. 
After this, take the square root to get the RMSD. 
It looks to me like QMol does something different. 
Thanks in advance, 
Richard 
  
> From Jason D. Gans: Hello, 
Qmol, available from the CCL software repository 
http://www.ccl.net/cca/software/MS-WIN95-NT/qmol/index.shtml 
can superimpose molecules and compute RMS deviation. 
Regards, 
Jason Gans 
B division 
Los Alamos National Lab 

-- 
Richard L. Wood, Ph. D. 
Physical/Computational Chemist 
  
  




From chemistry-request@ccl.net Fri Aug  8 14:11:32 2003
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Date: Fri, 8 Aug 2003 14:11:35 -0400 (EDT)
From: "Dr. Jan K Labanowski" <jkl|at|ccl.net>
To: =?iso-8859-1?Q?Mart=EDn?= Lema <mlema|at|unq.edu.ar>
cc: jkl|at|ccl.net, chemistry|at|ccl.net
Subject: Re: bug in quatfit???
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Dear CCL...

Martin Lema was kind to forward me the bug report on quatfit.c
Since there was a lot of talk on superimposing molecules, then
I'd rather post it to CCL. I corrected it in the CCL archives.
( http://www.ccl.net/cca/software/SOURCES/C/quaternion-mol-fit ).

Thank you Martin for finding this bug and letting me know. 

This was an unfortunate typo. It did not affect the results
when statistical weights where not given or equal to 1 (which
hopefully was the case for most of the calculations).

I am sorry for breaking this news, but better later than never.

Jan Labanowski
jkl|at|ccl.net


On Fri, 8 Aug 2003, [iso-8859-1] Martmn Lema wrote:

> Date: Fri, 08 Aug 2003 11:53:06 -0300
> From: "[iso-8859-1] Martmn Lema" <mlema|at|unq.edu.ar>
> To: jkl|at|ccl.net
> Subject: bug in quatfit???
> 
> Dear Mr. Labanowski:
> 
> 	I 4ve been using quatfit for a while, and I am not sure if there is a bug 
> in the programm. To be specific, I think that in line 913 of quatfit.c:
> 
> wnorm += s;
> 
> It should be:
> 
> wnorm += s*s;
> 
> I send you some files to check this.
  .... details deleted ...
> I also send you q2.c, the original quatfit.c file modified so line 913 is 
> wnorm += s*s. With this change in the source code, the programm behaves as 
> ( at least I ) expected.
> 
> I beg you to let me know if I am wrong in some way.
> 
> Sincerely
> 
> Martin

Jan K. Labanowski         |  phone: 614-292-9279,  FAX: 614-292-7168
Ohio Supercomputer Center |  E-mail: jkl|at|ccl.net 
1224 Kinnear Rd,          |  http://www.ccl.net/~jkl
Columbus, OH 43212-1163   |  http://www.ccl.net/    http://asdn.net/



From chemistry-request@ccl.net Fri Aug  8 12:57:09 2003
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Subject: a new question on comparing structures
Date: Fri, 8 Aug 2003 10:56:56 -0500
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Re: CCL:summary for program for superimposing (small)
Dear Per-Ola Norrby:

I understand your point. But I really don't want to compare wit X-rays, =
but to do a comparison
between calculated structures. Suppose, for example, that  I optimize =
the geometry of a molecule=20
with increasing basis set levels. Thus I have an STO-3G, 3-21G, 6-31G, =
6-311G optimized structures.=20
Then I calculate the RMSD between each of the structures and that coming =
> from the 6-311G=20
optimization (the highest level in this example). I guess that the RMSD =
is going to decrease  from=20
a maximum value for the STO-3G down to 0 corresponding to the 6-311G =
with itself.

Of course, the best match will be 0. But beside this, can we take a RMSD =
value (what I call the
threshold value in my previous message) and consider it closely enough =
to the best match ?
In order words, that the structure optimized with, say 6-31G, will be =
almost as good as 6-311G ?

I know that the example I has given is a very simple and moreover =
abstract one. That is why I
asked my question in the CCL hoping that the experience of the members =
with different
molecular geometry optimizations will help me. Of course, I understand =
the problem in terms
of listings of bonds and angles.

Thanks in advance

                                                           Daniel

**********************************************************************
Dr. Daniel Glossman-Mitnik
Centro de Investigaci=F3n en Materiales Avanzados (CIMAV)
LAQUICOM - Laboratorio de Qu=EDmica Computacional
Miguel de Cervantes 120 - Comp. Ind. Chihuahua
Chihuahua, Chih. 31109 - MEXICO
Tel.: (52) 614 4391151
FAX: (52) 614 4391112
E-mail: daniel.glossman{at}cimav.edu.mx
            glossman{at}hotmail.com
            dglossman{at}yahoo.com
**********************************************************************
  ----- Original Message -----=20
  From: Per-Ola Norrby=20
  To: Dr. Daniel Glossman-Mitnik=20
  Cc: chemistry{at}ccl.net=20
  Sent: Friday, August 08, 2003 5:41 AM
  Subject: Re: CCL:summary for program for superimposing (small) =
molecules and new question


          Dear Daniel,


    Before I present the summary, I was to ask the (neccessary)
    follow-up question:  In your experience, when a comparison
    of an experimental molecular structure (i.e. X-rays) and its
    calculated (Gaussian) counterpart is done, which will be the
    treshold RMSD value which can be considered acceptable ?


          The RMSD value is NOT a good measure of quality.  One reason =
is that soft modes (mainly torsions) are easily distorted by crystal =
packing, leading to huge discrepancies if you only look at RMSD.  A case =
in point is biphenyl, where the crystal adopts a planar structure =
becuase it packs better, whereas the gas phase global minimum has a =
torsion angle around 41 degrees.


          You can either use a comparison that is insensitive to these =
discrepancies, or do the calculation in the crystal (requiring QM with =
periodic boundaries, not in Gaussian).  I'd recommend comparison of =
lists of bond lengths and angles.  Alternatively, you can use the energy =
of the crystal structure calculated by Gaussian and compare it to the =
global minimum in Gaussian, but that requires constrained relaxation of =
the crystal structure to allow for differences in paradigm between X-ray =
and QM.


          Best regards,


          Per-Ola Norrby
--=20
Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/
  Technical University of Denmark, Department of Chemistry
  Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
  Email: pon{at}kemi.dtu.dk  tel +45-45252123,  fax +45-45933968
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<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Dear Per-Ola Norrby:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>I understand your point. But I really =
don't want to=20
compare wit X-rays, but to do a comparison</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>between calculated =
structures.&nbsp;Suppose, for=20
example, that &nbsp;I optimize the geometry of&nbsp;a molecule =
</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>with increasing </FONT><FONT =
face=3DArial=20
size=3D2>basis set levels.&nbsp;Thus I have an STO-3G, 3-21G, 6-31G, =
6-311G=20
optimized structures.&nbsp;</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Then I </FONT><FONT face=3DArial =
size=3D2>calculate the=20
RMSD between each of the structures and that coming from the 6-311G=20
</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>optimization </FONT><FONT face=3DArial =
size=3D2>(the=20
highest level in this example). I guess that the RMSD is going to =
decrease=20
</FONT>&nbsp;<FONT face=3DArial size=3D2>from </FONT></DIV>
<DIV><FONT face=3DArial size=3D2>a maximum </FONT><FONT face=3DArial =
size=3D2>value for=20
the STO-3G down to 0 corresponding to the 6-311G with =
itself.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Of course, the best match will be 0. =
But beside=20
this, can we take a RMSD value (what I call the</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>threshold value in my previous message) =
and=20
consider it closely enough to the best match ?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>In order words, that the structure =
optimized with,=20
say 6-31G, will be almost as good as 6-311G ?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>I know that the example I has given is =
a very=20
simple and moreover abstract one. That is why I</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>asked my question in the CCL hoping =
that the=20
experience of the members with different</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>molecular geometry optimizations will =
help me. Of=20
course, I understand the problem in terms</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>of listings of bonds and =
angles.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Thanks in advance</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial=20
size=3D2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
Daniel</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV>********************************************************************=
**<BR>Dr.=20
Daniel Glossman-Mitnik<BR>Centro de Investigaci=F3n en Materiales =
Avanzados=20
(CIMAV)<BR>LAQUICOM - Laboratorio de Qu=EDmica Computacional<BR>Miguel =
de=20
Cervantes 120 - Comp. Ind. Chihuahua<BR>Chihuahua, Chih. 31109 - =
MEXICO<BR>Tel.:=20
(52) 614 4391151<BR>FAX: (52) 614 4391112<BR>E-mail: <A=20
href=3D"mailto:daniel.glossman{at}cimav.edu.mx">daniel.glossman{at}cimav.edu.mx=
</A><BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;=20
<A=20
href=3D"mailto:glossman{at}hotmail.com">glossman{at}hotmail.com</A><BR>&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
<A=20
href=3D"mailto:dglossman{at}yahoo.com">dglossman{at}yahoo.com</A><BR>**********=
************************************************************</DIV>
<BLOCKQUOTE dir=3Dltr=20
style=3D"PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; =
BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
  <DIV style=3D"FONT: 10pt arial">----- Original Message ----- </DIV>
  <DIV=20
  style=3D"BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: =
black"><B>From:</B>=20
  <A title=3Dpon{at}kemi.dtu.dk href=3D"mailto:pon{at}kemi.dtu.dk">Per-Ola =
Norrby</A>=20
  </DIV>
  <DIV style=3D"FONT: 10pt arial"><B>To:</B> <A =
title=3Ddaniel.glossman{at}cimav.edu.mx=20
  href=3D"mailto:daniel.glossman{at}cimav.edu.mx">Dr. Daniel =
Glossman-Mitnik</A>=20
  </DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Cc:</B> <A =
title=3Dchemistry{at}ccl.net=20
  href=3D"mailto:chemistry{at}ccl.net">chemistry{at}ccl.net</A> </DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Sent:</B> Friday, August 08, 2003 =
5:41=20
  AM</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Subject:</B> Re: CCL:summary for =
program for=20
  superimposing (small) molecules and new question</DIV>
  <DIV><FONT face=3DArial size=3D2></FONT><FONT face=3DArial =
size=3D2></FONT><BR></DIV>
  <DIV><X-TAB>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </X-TAB>Dear=20
  Daniel,</DIV>
  <DIV><FONT face=3DArial size=3D2></FONT><FONT face=3DArial =
size=3D2></FONT><BR></DIV>
  <BLOCKQUOTE cite=3D"" type=3D"cite"><FONT face=3DArial =
size=3D-1>Before I present=20
    the summary, I was to ask the (neccessary)</FONT></BLOCKQUOTE>
  <BLOCKQUOTE cite=3D"" type=3D"cite"><FONT face=3DArial =
size=3D-1>follow-up=20
    question:&nbsp; In your experience, when a =
comparison</FONT></BLOCKQUOTE>
  <BLOCKQUOTE cite=3D"" type=3D"cite"><FONT face=3DArial size=3D-1>of an =
experimental=20
    molecular structure (i.e. X-rays) and its</FONT></BLOCKQUOTE>
  <BLOCKQUOTE cite=3D"" type=3D"cite"><FONT face=3DArial =
size=3D-1>calculated=20
    (Gaussian) counterpart is done, which will be =
the</FONT></BLOCKQUOTE>
  <BLOCKQUOTE cite=3D"" type=3D"cite"><FONT face=3DArial =
size=3D-1>treshold RMSD value=20
    which can be considered acceptable ?</FONT></BLOCKQUOTE>
  <DIV><FONT face=3DArial size=3D2></FONT><FONT face=3DArial =
size=3D2></FONT><BR></DIV>
  <DIV><X-TAB>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </X-TAB>The =
RMSD value=20
  is NOT a good measure of quality.&nbsp; One reason is that soft modes =
(mainly=20
  torsions) are easily distorted by crystal packing, leading to huge=20
  discrepancies if you only look at RMSD.&nbsp; A case in point is =
biphenyl,=20
  where the crystal adopts a planar structure becuase it packs better, =
whereas=20
  the gas phase global minimum has a torsion angle around 41 =
degrees.</DIV>
  <DIV><FONT face=3DArial size=3D2></FONT><FONT face=3DArial =
size=3D2></FONT><BR></DIV>
  <DIV><X-TAB>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </X-TAB>You can =
either=20
  use a comparison that is insensitive to these discrepancies, or do the =

  calculation in the crystal (requiring QM with periodic boundaries, not =
in=20
  Gaussian).&nbsp; I'd recommend comparison of lists of bond lengths and =

  angles.&nbsp; Alternatively, you can use the energy of the crystal =
structure=20
  calculated by Gaussian and compare it to the global minimum in =
Gaussian, but=20
  that requires constrained relaxation of the crystal structure to allow =
for=20
  differences in paradigm between X-ray and QM.</DIV>
  <DIV><FONT face=3DArial size=3D2></FONT><FONT face=3DArial =
size=3D2></FONT><BR></DIV>
  <DIV><X-TAB>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </X-TAB>Best=20
  regards,</DIV>
  <DIV><BR></DIV>
  <DIV><X-TAB>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </X-TAB>Per-Ola =

  Norrby</DIV><X-SIGSEP><PRE>--=20
</PRE></X-SIGSEP>
  <DIV>Per-Ola Norrby, Assoc. Professor,=20
  http://compchem.dfh.dk/PeO/<BR>Technical University of Denmark, =
Department of=20
  Chemistry<BR>Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, =
Denmark<BR>Email:=20
  pon{at}kemi.dtu.dk&nbsp; tel +45-45252123,&nbsp; fax=20
+45-45933968</DIV></BLOCKQUOTE></BODY></HTML>

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