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From: David Cerutti <dcerutti.mccammon.ucsd.edu>

Date: Wed, 14 Feb 2007 16:08:45 -0800 (PST)

Hello again,

I've been making some headway on this constraint virial problem, and I

now know that my error involves the computation of constraint forces for

SETTLE'd water molecules.

Does anyone know where I can find formula that tell you the forces to

apply along each of the three constrained bonds to reproduce the

accelerations that the SETTLE routine applies to the water? The problem

can be phrased fairly simply: SETTLE is considered to have applied forces

along each of the constrained bonds to return the molecule to its original

shape after a Verlet-integration (half) step deformed the water molecule

slightly. But, at the end of the SETTLE calculation, all we have are the

new velocities, from which we derive the net accelerations and thus the

net forces on each atom. Ww must account for these force vectors with a

unique set of forces acting along each of the bonds. Three constrained

bonds, three atoms and one net force on each atom resulting from the

SETTLE calculation.

But, when I try to write down these equations and then solve for the

magnitude of the force along each bond, I run into all sorts of trouble

and I can't figure out why. It would seem that the system is

over-determined; I can write nine different equations relating each of the

three components of the three net atomic forces computed by SETTLE to two

other terms involving the forces applied along each of the bonds ending at

each of the three atoms. I can pick three of the equations and solve them

for the magnitude of the force along each bond, but for some resaon I get

different results depending on which three equations I pick--they don't

even seem to be self-consist when I look closely at the equations.

But, at the same time, it seems that there are three unknowns (the

magnitudes of the forces along each bond) and three knowns (the net force

on each atom applied by SETTLE) so there should be a fairly concise

solution to these equations...

Thanks!

Dave

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Received on Sun Feb 18 2007 - 06:07:13 PST

Date: Wed, 14 Feb 2007 16:08:45 -0800 (PST)

Hello again,

I've been making some headway on this constraint virial problem, and I

now know that my error involves the computation of constraint forces for

SETTLE'd water molecules.

Does anyone know where I can find formula that tell you the forces to

apply along each of the three constrained bonds to reproduce the

accelerations that the SETTLE routine applies to the water? The problem

can be phrased fairly simply: SETTLE is considered to have applied forces

along each of the constrained bonds to return the molecule to its original

shape after a Verlet-integration (half) step deformed the water molecule

slightly. But, at the end of the SETTLE calculation, all we have are the

new velocities, from which we derive the net accelerations and thus the

net forces on each atom. Ww must account for these force vectors with a

unique set of forces acting along each of the bonds. Three constrained

bonds, three atoms and one net force on each atom resulting from the

SETTLE calculation.

But, when I try to write down these equations and then solve for the

magnitude of the force along each bond, I run into all sorts of trouble

and I can't figure out why. It would seem that the system is

over-determined; I can write nine different equations relating each of the

three components of the three net atomic forces computed by SETTLE to two

other terms involving the forces applied along each of the bonds ending at

each of the three atoms. I can pick three of the equations and solve them

for the magnitude of the force along each bond, but for some resaon I get

different results depending on which three equations I pick--they don't

even seem to be self-consist when I look closely at the equations.

But, at the same time, it seems that there are three unknowns (the

magnitudes of the forces along each bond) and three knowns (the net force

on each atom applied by SETTLE) so there should be a fairly concise

solution to these equations...

Thanks!

Dave

-----------------------------------------------------------------------

The AMBER Mail Reflector

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To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Sun Feb 18 2007 - 06:07:13 PST

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