Subject: Summary, Torsional MD

From: Yongxing Liu <[email-masked]>
Date: Thu, 2 Jul 1998 10:49:08 -0400 (EDT)

Dear Friends,

Thanks a lot for answering my question. Here is the summary of the answers. 

Thanks again!

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I want to know if there exists one program that can perform Molecular
Dynamics Simulation only in torsional space. I also want to know related
algorithms and the degree of difficulty to implement such a program compared
with normal Cartesian MD programs. I know some programs can do this by
restrain bond length and bond angles, but this will have extra cost. Please
correct me if I am wrong.
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I think Harold Scheraga's group published such an algorithm
at least 6 or 8 years ago. (sorry I don't have the ref anymore). 
I recall the theory reminded me of automatic Talyor series expansion methods
(Y.F. Chang, early 80's).

Richard

Cornell Theory Center
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> I think Harold Scheraga's group published such an algorithm
> at least 6 or 8 years ago. (sorry I don't have the ref anymore).
> I recall the theory reminded me of automatic Talyor series expansion methods
> (Y.F. Chang, early 80's).

The program is available from QCPE (qcp664).  Be careful though, we never got it
to compile because it requires some libraries we didn't have (and they cost $$).

Cheers
Michael
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Dear Yongxing,

As you probably know, most computation chemistry program uses Cartesian 
coordinates (XYZ) for 
modelling of molecule instead of internal coordinates (bond length, bond angles
and torsion angles). As I know, there are not program that operates internal
coordinates. But using cartesian coordinates for torsional space development is 
hard because program have to recalculate ALL coordinates for changing only
ONE torsion angle. On my opinion, for this principial reason calculating
of torsional space in cartesian coordinates should have unsatisfactory 
accuracy.

Now we are attempting to write program that uses internal coordinates, but
even alpha version is not ready today.

Vladimir.
"Tikhonenko Vladimir" <[email-masked]>
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Hi,
Just a quick note... try looking at a package called ICM. A wb search
should pull it up.

Cheers
Ashley
From: Ashley George <[email-masked]>
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check out Axel Bruenger's X-plor, they recently implemented torsion angle
dynamics for protein structure refinement:

Proteins 1994 Aug;19(4):277-290 

Torsion angle dynamics: reduced variable conformational sampling
enhances crystallographic structure refinement.

Rice LM, Brunger AT

Cheers,

Ronald

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the program XPLOR can perform torsion angle dynamics. Find info re XPLOR at

	http://www.NMR.EMBL-Heidelberg.DE/xplor/htmlman/
or at
	http://xplor.csb.yale.edu/xplor-info/xploronline.html

The torsion dynamics part is described in a draft manuscript which seems
not to have made it into the main docs so far. You might be interested in
the references mentioned therein:

1) Bac, D.-S. and Haug, E.J. (1987) Mech. Struct. Mach. 15:359-382
2) Bac and Haug (1987),  Mech. Struct. Mach. 15:481-506
3) Rice, L.M. and Bruenger, A.T. (1994) Proteins 19:277-290

The last reference is probably the most interesting for you.

Regards,
	
	Lutz Ehrlich
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Lutz Ehrlich		email:	[email-masked]
EMBL			web  :  http://www.embl-heidelberg.de/~ehrlich
Meyerhofstr. 1		
D-69012 Heidelberg	phone: +49-6221-387-140
Germany			fax  : +49-6221-387-517

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You might be interested in these two papers:

    G.R. Kneller, K. Hinsen
    Generalized Euler equations for linked rigid bodies
    Phys. Rev. E 50, 1559 (1994)

    K. Hinsen, G.R. Kneller
    Influence of constraints on the dynamics of polypeptide chains
    Phys. Rev. E 52, 6868 (1995)

The first paper derives the equations of motions for a system with
arbitrary distance constraints using generalized coordinates (torsion
angle dynamics is a special case). The second paper presents an
implementation and application. The implementation is available as a
set of Fortran subroutines that should be easy to integrate into any
MD program (we used an old version of Gromos); write to me if you are
interested. Please note that I didn't spend much effort to optimize
the implementation. In my experience, constraint-type dynamics, in
whatever way it is implemented, does not work well for significantly
reduced coordinate sets, and is of little advantage for
almost-complete coordinate sets, so I didn't want to invest any more
effort.

Another paper that could be of interest for you is

    L.M. Rice, A.T. Br"unger
    Torsion Angle Dynamics: Reduced Variable Conformational
    Sampling Enhances Crystallographic Structure Refinement
    Proteins 19, 277 (1994)

It describes protein dynamics in phi-psi space (i.e. a subset of
torsional angle space) for use in structure refinement, i.e. simulated
annealing. For that application, the correctness of the dynamics is
unimportant, so rather drastic constraints can be useful. But then
you might be better off with some Monte-Carlo method if you don't
care about dynamics. I suppose this method is implemented in some
version of XPlor.
-- 
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Try the following programs:
http://www.scsb.utmb.edu/fantom/
http://dasher.wustl.edu/tinker/
This is a good software list:
http://antas.agraria.uniss.it/software.html
hope this helps,

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Yongxing Liu, Graduate Student | E-Mail: [email-masked]
Department of Chemistry        | Tel.:   860-685-2777 
Wesleyan University            | Fax:    860-685-2211 
Middletown CT 06457            | URL:
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