Subject: Re: CCL:Help on force field for simplified "atoms"

From: "Rebecca Rone" <[email-masked]>
Date: Tue, 31 Oct 2000 10:36:45 -0600

Dear Guosheng,

Your approach will probably not work in most cases. The C6H6 group needs to
be able to stack in order to create correct interactions. There are several
examples of this in the literature on x-ray structures. The most famous is
the herringbone arrangement of benzene and there are several similar
interactions for drugs with proteins. I cannot recommend  this approach.
Please see the Momany & Rone paper on force field development :

"Validation of the General Purpose QUANTA 3.2/CHARMm Force Field," J. Comp.
Chem. 13 (7), 888-900 (1992).

Also check the MSI web site for other related information. This forcefield
is currently in use for QUANTA and their CNX product. Friends inform me that
it currently provides extensive coverage for drugs interacting with
proteins.

Becky
Dr. Rebecca Rone
Rone Biotechnology Consulting
773-646-2585
Chicago, IL.
Boston, MA.

----- Original Message -----
From: "Guosheng Wu" <[email-masked]>
To: "ccl" <[email-masked]>
Sent: Monday, October 23, 2000 4:16 PM
Subject: CCL:Help on force field for simplified "atoms"

> Dear folks,
>
> Does any of you have the experience on developing force field for
> simplified "atoms"?
>
> I know there are some papers related with simplified "atom" for CH2
> or CH3, but how about biger molecules?
>
> For example, if I want to get a simple function V(R) for the interction
> between C6H6 and C6H6, I may either summarize the LJ(rij) interctions
> between all of atoms(i in one molecule and j in the other one), or I can
> do ab initio calculations for different intermolecular distances(R). By
> both methods I may be able to fit the results into a simple function, say
> still in LJ(R) form.  However, sometimes this mayn't work, or very
> time-consuming for big molecules.
>
> If anyone could give me some suggestions or related reference, I will be
> very grateful.
>
> Thanks a lot!
>
> Guosheng Wu
> --------------------------------------------
> Guosheng Wu
> Dept. of Chem.,  Northwestern Univ.
> 2145 Sheridan Road, Evanston, IL, 60208-3113
> --------------------------------------------
>
>
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---

From: Harald Svedung <[email-masked]>
Date: Mon, 30 Oct 2000 19:12:12 +0100

Hi,

I think this question i very interesting. Indeed there is a need for
simple "V(R)-functions" in various contexts. (is there not?... tell me.)

The problem with C6H6 and pairwise atom-atom interactions is that the C6H6
molecule shows some quite "non-atomic" or "molecular" qualities (aromatic
interaction, anisotropic polarizabilities etc). Theese features are
averaged out only at large distances using any atomic potential.

Atom-atom LJ(rij) contributions can be taken from the literature as a
first-aid in building a potential function. These parameters are not able
to represent (in general) the specific qualities of, e.g.,
C6H6.

LJ(12-6) potentials often over-estimate the repulsive hardness of
the atom-atom interactions and there is no explicit treatment of the
electrostatics. Therefore the mapping of ab-initio potential energy to
such a potential must be done with care taken to the energies of interest 
and also to the angle of approach.

Maby a single center angular dependent Buckingham-type (exp-6) potential
would do as a first approximation, perhaps with the hydrogens interacting
explicitly (...any other suggestions)

all yours :-)
/Harald

On Tue, 31 Oct 2000, Rebecca Rone wrote:

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> 
> 
> 
> 
>

---

From: Guosheng Wu <[email-masked]>
Date: Mon, 30 Oct 2000 17:53:49 -0600 (CST)

Hi, all,

As the request of a few people, I am summarizing what I got on this topic.
Sorry for those who are n't interested, but have to get it. :-)

First of all, I recommend a new book by A. F. Sax(editor), 

 "Potential energy surfaces"  (Springer, 1999)
               ----- Lecture notes in Chemistry  (71)

and one reference in the book (page 204, ref h, missing for some reason).
  M. A. Bates & G. R. Luckhurst, J. Chem. Phys., 104(17), 6696, 1996

The book is very useful for those who are interested in potential energy
surface and force field development. The paper is on "anisotropic 
version of a shifted LJ potential", with application in the simulation of
liquid crystals. (This may be the most related reference.)

Then, here are the responses I have got so far.(only 4, :-)

--(1)-------------------------------------------------------------------------
Date: Tue, 24 Oct 2000 11:22:18 +1000
From: "Kieran F Lim (Lim Pak Kwan)" <[email-masked]>

groups like CH2 and CH3 are *relatively* (not perfectly) spherically
symmetric so the unified atom (simplified "atom") approach is
justified. 

however, groups like C6H5 (phenyl) or molecules like C6H6 (benzene)
have a big orientation dependence (ie anisotropy) and cannot be modelled
satisfactorily by a distance-dependent LJ(R) form without additional
orientation (angle-dependent) terms. the best *simple* approach is to
use atom-atom terms.

we have looked at benzene-atom interactions in the context of
atom-molecule collision dynamics. the calculations, etc of the
potential function may help you in your thoughts

T. Lenzer, K. Luther, J. Troe, R. G. Gilbert and K. F. Lim,
"Trajectory simulations of collisional energy transfer in highly excited
benzene and hexafluorobenzene",
Journal of Chemical Physics, 1995, 103 (2), 626-641.

Kieran

---(2)------------------------------------------------------------------------
From: Keith Glassford <[email-masked]>
Subject: Re: Fwd: Re: Fwd: CCL:Help on force field for simplified
Date: 10/24/00 4:41 PM

What he wants to do is coarse grain the potentials and yes MSI does have
experience in this and we have a product called Dissipative Particle
Dynamics or DPD. One can use the COMPASS force field, blends, amorphous
builder, dynmics etc, to get the interaction parameters needed for these
simulations. Please direct him to the DPD site:

http://www.msi.com/materials/cerius2/DPD.html

and especially the following example which illustrates an oil water
interface:

http://www.msi.com/materials/cases/oilwater.html

The usefulness of DPD will depend upon what type of system he wants to
investigate and the chemistry and physics he is after.

Best wishes,

Keith

***(3)************************************************************************
Date: Tue, 31 Oct 2000 10:36:45 -0600
From: Rebecca Rone <[email-masked]>

Your approach will probably not work in most cases. The C6H6 group needs
to
be able to stack in order to create correct interactions. There are
several
examples of this in the literature on x-ray structures. The most famous is
the herringbone arrangement of benzene and there are several similar
interactions for drugs with proteins. I cannot recommend  this approach.
Please see the Momany & Rone paper on force field development :

"Validation of the General Purpose QUANTA 3.2/CHARMm Force Field," J.
Comp.
Chem. 13 (7), 888-900 (1992).

Also check the MSI web site for other related information. This forcefield
is currently in use for QUANTA and their CNX product. Friends inform me
that
it currently provides extensive coverage for drugs interacting with
proteins.

Becky
Dr. Rebecca Rone
Rone Biotechnology Consulting
773-646-2585
Chicago, IL.
Boston, MA.
****(4)*************************************************************************

Date: Mon, 30 Oct 2000 19:12:12 +0100
From: Harald Svedung <[email-masked]>

all yours :-)
/Harald
******************************************************************************

Finally, thanks a lot to those who responsed, gave reference or
suggestion. More discussion is highly appreciated.

Best regards!

Guosheng