Subject: Summary: MD parameters from ab initio calculations

From: Christoph Heidelbach <[email-masked]>
Date: Mon, 25 Mar 1996 10:53:32 +0100

Dear CCL'ers,

many thanks to all those who answered me. My original question was:

I am searching for some information about the evaluation of force field 
parameters for molecular dynamics from ab initio or semiempirical calculations.
What I am looking for is how to fit atomic charges and Lennard-Jones-parameters.
Any answers will be greatly appreciated and I will summerize all replies.

This is what I got:

>From [email-masked] Tue Feb 27 22:04 MEZ 1996
Date: Tue, 27 Feb 1996 16:03:34 -0500
To: [email-masked]
Subject: Re: CCL:MD parameters from ab initio
>From: [email-masked] (Konrad HINSEN)
Status: RO

   I am searching for some information about the evaluation of force field 
   parameters for molecular dynamics from ab initio or semiempirical calculations.
   What I am looking for is how to fit atomic charges and Lennard-Jones-parameters.

Ich schreiben gerade an einem Artikel ueber ein solches Projekt (ein
Potential fuer quantenmechanische Simulationen von Protonentransfer in
Acetylaceton), mit einer recht ausfuehrlichen Abhandlung ueber das
Fitten von Ladungen, da meine Methode sich von den ueblichen
unterscheidet. Ich kann gerne eine Kopie (auch elektronisch) schicken,
wenn alles fertig ist, d.h. voraussichtlich naechste Woche.

-------------------------------------------------------------------------------
Konrad Hinsen                     | E-Mail: [email-masked]
Departement de chimie             | Tel.: +1-514-343-6111 ext. 3953
Universite de Montreal            | Fax:  +1-514-343-7586
C.P. 6128, succ. Centre-Ville     | Deutsch/Esperanto/English/Nederlands/
Montreal (QC) H3C 3J7             | Francais (phase experimentale)
-------------------------------------------------------------------------------

>From [email-masked] Tue Feb 27 22:22 MEZ 1996
>From: "Erin Duffy" <[email-masked]>
Subject: Re: CCL:MD parameters from ab initio
To: [email-masked] (Christoph Heidelbach)
Date: Tue, 27 Feb 1996 16:21:56 -0500 (EST)
Status: RO

Hi -  I'd suggest looking at some of Bill Jorgensen's
      papers - his group are experts in this area.  Here
      is a small sampling.  Please contact me if I can
      be of further assistance.  - Erin Duffy
                                 [email-masked]

Jorgensen, W.L.; Madura, J.D.; Swenson, C.J.  "Optimized
Intermolecular Potential Functions for Liquid Hydrocarbons."
J. Am. Chem. Soc., 1984, v.106, 6638-6646.

Jorgensen, W.L.; Tirado-Rives, J.  "The OPLS Potential Functions
for Proteins.  Energy Minimizations for Crystals of Cyclic
Peptides and Crambin."  J. Am. Chem. Soc., 1988, v.110, 1657-1666.

Jorgensen, W.L.; Gao, J.  "Cis-Trans Energy Difference for the
Peptide Bond in the Gas Phase and in Aqueous Solution."  J. Am.
Chem. Soc., 1988, v.110, 4212.

Jorgensen, W.L.; Severance, D.L.  "Aromatic-Aromatic Interactions:
Free Energy Profiles for the Benzene Dimer in Water, Chloroform,
and Liquid Benzene."  J. Am. Chem. Soc., 1990, v.112, 4768-4774.

Duffy, E.M.; Severance, D.L.; Jorgensen, W.L.  "Urea:  Potential
Functions, logP, and Free Energy of Hydration."  Isr. J. Chem.,
1993, v.33, 323-330.

Carlson, H.A.; Nguyen, T.B.; Orozco, M.; Jorgensen, W.L.  "Accuracy
of Free Energies of Hydration for Organic Molecules from 6-31G(d)-
Derived Partial Charges."  J. Comput. Chem., 1993, v.14, 1240-1249.

>From [email-masked] Wed Feb 28 02:05 MEZ 1996
Date: Tue, 27 Feb 1996 17:05:16 -0800
>From: [email-masked] (Masahiko Katagari XPIRE 4-15-96 HOST John Newsam Tohoku University)
Message-Id: <[email-masked]>
To: [email-masked]
Subject: MD parameters
Status: RO

Dear Dr. Christoph Heidelbach,

As for the parametrization, we (biosym/msi) parametrize the LJ and partial
charge using a nonlinear least-squares fit to the ab-initio data.
If you are interested in, please refer, e.g.

	J.Hill and J.Sauer,
	Molecular Mechanics Potential for Silica and Zeolite Catalysis
	Based on ab initio Calculations.
	1. Dens and Microporous Silica

	J. Phys. Chem. 98, 1238 (1994).

This method produces the potential which includes many body terms such as
distortion. The charges in the forcefield are directly taken from a population
analysis of the wavefunctions. The use of charges is somewhat artificial, since
potential has its origin in a Taylor series expansion which accounts for all
interactions. In this context, point charge interactions are not required,
but because of the necessity to describe interactions between atoms or groups
which are not directly connected by bonds, but which may come close to each
other simulations, they are introduced in potential, too.

Frankly speaking, we use the partial charge as a parameter to fit the
experimental data.

As for the repulsive van der Waals parameters, test particle method is
frequently used.

See for example,

	H. Bohm and R. Ahlrichs
	A Study of short-range repulsions.

	J. Chem. Phys., 77, 2028 (1982).

or

	H. Bohm, R. Ahlrichs, P. Scharf and H. Schiffer
	Intermolecular potentials for CH4, CH3F, CHF3, CH3Cl, CH2Cl2, CH3CN and CO2

	J. Chem. Phys., 81, 1389 (1984).

Best Regards,

Masa Katagiri

 __o__o_o__o __o    Masahiko Katagiri            __o__o_o__o __o
`\<,\<,<,\<,`\<,    [email-masked]             `\<,\<,<,\<,`\<,
O/ O/ O O/ OO/ O    TEL -1-619-546-5389(direct) O/ O/ O O/ OO/ O
                    FAX -1-619-458-0136
                    e_mail  [email-masked]
                                                                         
             MSI  9685 Scranton Road  San Diego, CA 92121

>From [email-masked] Wed Feb 28 02:13 MEZ 1996
Date: Tue, 27 Feb 1996 17:13:37 -0800 (PST)
>From: [email-masked]
Message-Id: <[email-masked]>
To: [email-masked]
Subject: Re:  CCL:MD parameters from ab initio
Status: RO

You might want to check out the force field sections
of the amber web pages at:

  http://www.amber.ucsf.edu/amber/

Bill Ross

>From [email-masked] Wed Feb 28 09:21 MEZ 1996
Date: Wed, 28 Feb 1996 09:19:25 +0100
To: Christoph Heidelbach <[email-masked]>,
        [email-masked]
>From: [email-masked] (Pascal HEBANT)
Subject: Re: CCL:MD parameters from ab initio
Cc: [email-masked]
Status: RO

At 18:57 27/02/96, Christoph Heidelbach wrote:
>Hallo everybody out there,
>
>I am searching for some information about the evaluation of force field
>parameters for molecular dynamics from ab initio or semiempirical calculations.
>What I am looking for is how to fit atomic charges and
>Lennard-Jones-parameters.
>Any answers will be greatly appreciated and I will summerize all replies.
>
>Best regards.
>
>Christoph
>

We have done something like that in our lab : we have computed pair
potential function of Born Huggins Mayer type with DMol calculations :
Point energies are performed for the 2 atoms involved in the potential with
fixed geometry. Then, a curve fitting (with Kaleidagraph) allowed us to
obtain the parameters.
See e.g.  Roullet, G., J. J. Legendre, et al. (1994). "Ab-initio and
molecular dynamics studies of molten NaCl Graphite interfaces." Molten Salt
Forum 1-2: 105-116.

Hope this helps you

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 (1) 44 27 66 94                             fax: 33 (1) 44 27 67 50

http://alcyone.enscp.jussieu.fr/Pages/LECA/Electrochimie.html
*****************************************************************************

>From [email-masked] Wed Feb 28 09:50 MEZ 1996
>From: "Ferenc Molnar" <[email-masked]>
Message-Id: <[email-masked]>
Date: Wed, 28 Feb 1996 09:50:11 +0100
In-Reply-To: Christoph Heidelbach <[email-masked]>
        "CCL:MD parameters from ab initio" (Feb 27,  6:57pm)
References: <[email-masked]>
X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail)
To: Christoph Heidelbach <[email-masked]>
Subject: Re: CCL:MD parameters from ab initio
Content-Type: text/plain; charset=us-ascii
Mime-Version: 1.0
Status: RO

Hallo Chrisoph!

> What I am looking for is how to fit atomic charges and
> Lennard-Jones-parameters.
> Any answers will be greatly appreciated and I will summerize all replies.

Das wuerde mich auch sehr interessieren! Bitte schick mir doch
die Antworten, insbesondere Hinweise auf bestehende Programme!

Einige Referenzen kann ich dir geben:

1) N.L. Allinger and J.P. Bowen in Rev.Comp.Chem. 2, K.B. Lipkowitz
and D.B. Boyd (Eds.), VCH, 1991, ISBN 3-527-28338-2.

2) U. Dinur and A.T. Hagler (ebd.).

3) AUTHOR = {G. Chalasi\'nski and M.M. Szcze\'sniak},
TITLE = {Origins of Structure and Energetics of van der Waals
 JOURNAL =Chem. Rev.,
YEAR = {1994},
VOLUME = {94},
NUMBER = {7},
PAGES = {1723--1765},
KEYS = {van der Waals, ab initio, dispersion, correlation, PES},

4) AUTHOR = {J.R. Maple and M.-J. Hwang and T.P. Stockfisch and
          U. Dinur and M. Waldman and C.S. Ewig and A.T. Hagler},
TITLE = {Derivation of Class II Force Fields. I. Methodology and
         Quantum Force Field for the Alkyl Functional Group and
         Alkane Molecules},
JOURNAL =J. Comp. Chem.,
YEAR = {1994},
VOLUME = {15},
NUMBER = {2},
PAGES = {162--182},
KEYS = {derivatives, parameters, ab initio, PES, anharmonicity,
        intramolecular forces, cross terms, transferability, validity },
        Clusters from ab Initio Calculations},

5) AUTHOR = {D.E. Woon},
 TITLE = {Accurate modeling of intermolecular forces: a systematic
         M\o ller-Plesset study of the argon dimer using correlation
         consistent basis sets},
JOURNAL = Chem. Phys. Lett.,
YEAR = {1993},
VOLUME = {204},
NUMBER = {1,2},
PAGES = {29--35},
KEYS = { PES, MP4, augmented correlation consistent basis set, argon,
         supermolecule approach, BSSE, CP},

Ich habe auch schon einige Parametrisierungsversuche unternommen.
Allerdings geraet man sehr schnell an die Grenzen der ab initio
Prgramme (Gaussian, Gamess) oder der Optimierungsverfahren (zu
viele Parameter). Eine Parametrisierung kann selbst fuer kleine Systeme
sehr aufwendig werden!

Trotzdem: Have fun!

Ferenc

>From [email-masked] Wed Feb 28 10:07 MEZ 1996
Date: Wed, 28 Feb 1996 09:19:25 +0100
To: Christoph Heidelbach <[email-masked]>,
        [email-masked]
>From: [email-masked] (Pascal HEBANT)
Subject: CCL:MD parameters from ab initio
Cc: [email-masked]
Sender: Computational Chemistry List <[email-masked]>
Errors-To: [email-masked]
Precedence: bulk
Status: RO

At 18:57 27/02/96, Christoph Heidelbach wrote:
>Hallo everybody out there,
>
>I am searching for some information about the evaluation of force field
>parameters for molecular dynamics from ab initio or semiempirical calculations.
>What I am looking for is how to fit atomic charges and
>Lennard-Jones-parameters.
>Any answers will be greatly appreciated and I will summerize all replies.
>
>Best regards.
>
>Christoph
>

We have done something like that in our lab : we have computed pair
potential function of Born Huggins Mayer type with DMol calculations :
Point energies are performed for the 2 atoms involved in the potential with
fixed geometry. Then, a curve fitting (with Kaleidagraph) allowed us to
obtain the parameters.
See e.g.  Roullet, G., J. J. Legendre, et al. (1994). "Ab-initio and
molecular dynamics studies of molten NaCl Graphite interfaces." Molten Salt
Forum 1-2: 105-116.

Hope this helps you

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 (1) 44 27 66 94                             fax: 33 (1) 44 27 67 50

http://alcyone.enscp.jussieu.fr/Pages/LECA/Electrochimie.html
*****************************************************************************

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>From [email-masked] Wed Feb 28 11:34 MEZ 1996
Date: Wed, 28 Feb 1996 10:38:40 +0000
To: [email-masked]
>From: [email-masked] (Darren Andrews)
Subject: Re: CCL:MD parameters from ab initio
Status: RO

A very basic way to do this would be to use the Mulliken or similar charges
from the Ab Initio output and some empirical Lennard-Jones parameters e.g.,
Lorentz-Berthelot to get a pretty rough set of starting values.
If you use a distributed multipole analysis approach (see Anthony Stone
circa. '89) which can be calculated using CADPAC you can get a (very) good
approximation of the electrostatic part of the interaction.  If the system
you are looking at is dominated by electrostatic forces then the empirical
L-J parameters will be less important.

Darren Andrews.

University of Manchester,
Department of Chemistry,
Oxford road,
Manchester.
M13 9PL.

[email-masked]
PGP: 512/62A971A9

Tel: 0161 275  2000 ext.4699.
Fax: 0161 275 4598.

>From [email-masked] Wed Feb 28 13:33 MEZ 1996
Date: Wed, 28 Feb 1996 09:32:46 -0300 (GRNLNDST)
>From: edgardo garcia <[email-masked]>
To: Christoph Heidelbach <[email-masked]>
Subject: Re: CCL:MD parameters from ab initio
In-Reply-To: <[email-masked]>
Message-Id: <[email-masked]>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
Status: RO

Hi Christoph,

	CHARGES

I'm currently using AM1 CHELP Potential derived charges that reproduce
the molecular dipoles with 12% error, usually bigger dipoles.
The dipoles are similar to the ones obtained from 6-31G* on the same
compounds. I also tried Charge Equilibration Method of Antony Rappe
but the results are really bad, not only the dipoles are wrong in 
absolute values but the trends for a set of molecules is also wrong.
The AM1 dipole trends are also correct.
The problem with force fields is that you need fixed charges, now
charges change with the connectivity environment and also (but much less 
important) with the 3D environment. I use AM1 charges computed for
model compounds and then I symmetrize the charges, by a simple average of 
the values of topologicaly identical atoms. 
With this fixed 2D AM1 CHELP charges I then parametrize the Force Field
to reproduce energy data.
There is no point in trying to be more accurate on that unless you can
use hyper-atom-types that embody the atom molecular environment.

	VdW

The vdW parameters are another story :-( 
I don't really know what is a good method. The points are:

- what do you want ?
- what is the quality/cost ratio for the method ? Is is worth it ?

I'm using OPLS vdW parameters and they are fixed for specific atom types.
>From my point of view one of the most serius works for liquid phases.
Again for organic molecules, I bet you that the vdW parameters will
change a bit depending on the atom environment. It could be that some
ab initio procedure can give you a good functional form and good parameters,
considering the BSSE was removed, but the problem is :
can you really make use of this great accuracy in your force field ?
You have to consider that force fields use limited atom types and
also there are the vdW combination rules, ad hoc little formulas,
who know were they really work ?
There is a nice work for noble gases for the ab initio derivation of vdW 
parameters, functional forms and combination rules. I don't remember
the reference now but I can give it to you latter if you are interested.
The author is A.T. Hagler from Merk, I think it was on JACS, 1985 - 1993.

The big deal will be to find parameters that are independent of the 
environment, i.e., pure parameteres. The big problem is what are good
functional forms, how the parameters change with topological and with 3D 
environment and how to include this in a usefull Force Field that is able 
to handdle them to make practical and accurate predictions.

Hope this helps,

Edgardo

Dr.Edgardo Garcia
Dpto of Chemistry
University of Brasilia,
Brasilia DF, Brazil

>From [email-masked] Thu Feb 29 16:53 MEZ 1996
>From: cheidel <[email-masked]>
Message-Id: <[email-masked]>
Subject: Re: CCL:MD parameters from ab initio (fwd)
To: [email-masked]
Date: Thu, 29 Feb 1996 16:52:41 +0100 (MET)
X-Mailer: ELM [version 2.4 PL25]
Content-Type: text
Content-Length: 3637
Status: RO

Forwarded message:
>From [email-masked] Wed Feb 28 23:30:32 1996
Delivery-Date: Wed, 28 Feb 1996 23:30:32 +0100
Message-Id: <[email-masked]>
Date: Wed, 28 Feb 1996 14:25:37 -0800 (PST)
>From: Joerg Hill <[email-masked]>
To: [email-masked]
Subject: Re: CCL:MD parameters from ab initio

Hallo,
> I am searching for some information about the evaluation of force field 
> parameters for molecular dynamics from ab initio or semiempirical
calculations.
> What I am looking for is how to fit atomic charges and
Lennard-Jones-parameters.
> Any answers will be greatly appreciated and I will summerize all replies.

Es gibt eine ganze Serie von Arbeiten ueber die Ableitung von repulsiven
van-der-Waals-Parametern aus ab initio Rechnungen von Boehm und Ahlrichs:

@article{boe82,
  author={H.-J.~B{\"o}hm and R.~Ahlrichs},
  title={A study of short--range repulsions},
  journal={J. Chem. Phys.},
  year=1982,
  volume=77,
  pages=2028
}
@article{boe84:1,
  author={H.-J.~B{\"o}hm and R.~Ahlrichs and P.~Scharf and H.~Schiffer},
  title={Intermolecular potentials for {CH$_4$, CH$_3$F, CHF$_3$,
CH$_3$Cl, CH$_2$Cl$_2$, CH$_3$CN, and CO$_2$}},
  journal={J. Chem. Phys.},
  year=1984,
  volume=81,
  pages=1389
}
@article{sag87,
  author={K.~P.~Sagarik and R.~Ahlrichs},
  title={A test particle model potential for formamide and molecular
dynamics simulations of the liquid},
  journal={J. Chem. Phys.},
  year=1987,
  volume=86,
  pages=5117
}
@article{sag86:1,
  author={K.~P.~Sagarik and R.~Ahlrichs and S.~Brode},
  title={ },
  journal={Mol. Phys.},
  year=1986,
  volume=57,
  pages=1247
}
@article{boe84:2,
  author={H.-J.~B{\"o}hm and C.~Meissner and R.~Ahlrichs},
  title={ },
  journal={Mol. Phys.},
  year=1984,
  volume=53,
  pages=651
}
@article{sag86:2,
  author={K.~P.~Sagarik and R.~Ahlrichs},
  title={ },
  journal={Chem. Phys. Letters},
  year=1986,
  volume=131,
  pages=74
}

Ich selbst habe vor kurzem ein Paper bei J. Comp. Chem. eingereicht, in
dem auch die
dispersiven Parameter aus ab initio Rechnungen abgeleitet werden. Ich
hoffe, das ich
bald Nachricht ueber die Annahme bekomme.

Viele Gruesse nach Deutschland
Joerg-R. Hill

-------------------------------------------------------------------------------
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Dr. Joerg-Ruediger Hill   | Every attempt to employ mathematical methods in the
Biosym/MSI                | study of chemical questions must be considered pro-
9685 Scranton Road        | foundly irrational  and  contrary  to the spirit of
San Diego, CA 92121-2777  | chemistry ...  If mathematical analysis should ever
USA                       | hold a prominent place in chemistry - an aberration
                          | which  is  happily  almost  impossible  -  it would
Phone (619) 546-5508      | occasion  a rapid  and  widespread  degeneration of
Fax   (619) 458-0136      | that science.
E-mail [email-masked]     |     Auguste Comte, Philosophie Positive,
Paris, 1838
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