Subject: trajectory

From: Rino Ragno <[email-masked]>
Date: Mon, 6 Apr 1998 21:47:45 -0500 (CDT)

Hi,

here there is a geometrical question.

Given the initial(A) and final(B) geometry of two conformation of a protein
how can I generate the trajectory of the interconversion A <-> B and store
the intermediate files, say for istance 20 conformation?

Is any of you out there aware of a program that solve the above problem.

I will summarize
Thanks a lot to all

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From: Richard Gillilan <[email-masked]>
Date: Wed, 08 Apr 1998 11:37:11 -0400

> Is any of you out there aware of a program that solve the above problem.

Obtaining actual trajectories connecting initial and final conformations
is a problem in variational calculus (of great interest in Semiclassical
calculations and other areas). I have a paper in JCP some years
ago that describes what I call the "Variational Verlet" method, which is
quite simple in concept but leads to equations that are difficult to
solve globally. The problem is that trajectories of any significant 
length are generally saddle points in the multidimensional space of 
of possible solutions rather than minima or maxima. This is a fundamental
problem that you will encounter with any such calculation that gives a true
trajectory. Back when I did my calculations in 1992, I worked with only 
about 100 atoms and finding convergent solutions was difficult but not
impossible. The theory does have some very interesting properties: there 
is formally NO accumulation of integration error with time (sounds impossible
doesn't it? One pays for it in other ways I suspect). Bill Hoover at Livermore
has introduced Lagrange multipliers into the equations to obtain true
nonequilibrium const Temp trajectories. Here are the papers:

"Shadowing, rare events and rubber bands. A variational Verlet algorithm
for molecular dynamics", Richard E. Gillilan and Kent R. Wilson
J. Chem Phys. 97 (3) 1 Aug 1992

William Hoover Phys Lett A vol 204 p133 (1995)

Sorry, the code was rather specialized and not designed for biomolecules,
perhaps someday I'll integrate it with my simulation suite
that uses MMFF94. 

If you don't need true trajectories, I suggest you look at Ron Elber's
work on reaction path calculations. His code is publically available
and works with proteins:

R. Czerminski and R. Elber, Int. J. Quant. Chem. 24, 167 (1990)

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From: Philippe Youkharibache <[email-masked]>
Date: Wed, 08 Apr 1998 11:08:19 -0700

> the intermediate files, say for istance 20 conformation?

The simplest is to run an MD trajectory with distance (and maybe other)
constraints
starting with your initial conformation while constraints are extracted
>from your final conformation

> Is any of you out there aware of a program that solve the above problem.

any MD program such as CHARMM or Discover or other

Philippe
 
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