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

Date: Tue, 13 Feb 2007 02:22:20 -0800 (PST)

I'm still having some problems with my barostat, but I've been able to

isolate the problem to the constraint virial **.

Can anyone with experience programming a calculation of the constraint

virial (preferably in the context of Velocity-Verlet integration) please

reply to my private email so we can discuss the finer points of the

algorithm and hopefully resolve my dilemma?

Dzeinkuje,

Dave

*>>>>>>>>>>>>>>>>>>>>>>>>>>
*

** Proof of point:

- When I simulate an ideal gas, my barostat takes the system to the

correct volume given the applied external pressure (this means that the

kinetic energy term in the pressure calculation is correct).

- When I simulate a Lennard-Jones gas with a sizeable epsilon parameter,

my computed energies are in close agreement (1%) with AMBER and the

final system volume is within 0.3% of that obtained by AMBER. I think

there must still be some long-range correction running around that I can't

quite get rid of, but the essential result is that my code and AMBER

produce very similar final volumes for this gas system, and those final

volumes are a significant (12-fold decrease) departure from the volume of

a similar amount of an ideal gas. So, the non-bonded virial (at least in

the case of monatomic particles) is correct.

- When I simulate a system of TIP3P water molecules without using SETTLE

but rather a crude system of bonds between O-H1, O-H2, and H1-H2, the

system also reaches a reasonable and stable final volume, close to a

density of 1.0 g/cm3 (it is reasonable at this point to assume that any

deviation is a result of not making the molecules rigid). So, the

non-bonded virial, again, is correct, and I can simulate tri-atomic

molecules under NPT conditions without trouble.

- When I try to simulate TIP3P water (or any other three-site water) with

SETTLE for rigid molecules, the system blows up (slowly but exponentially,

it expands until a numerical catastrophe hits). My constraint virial is

therefore obviously the problem.

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Received on Wed Feb 14 2007 - 06:07:37 PST

Date: Tue, 13 Feb 2007 02:22:20 -0800 (PST)

I'm still having some problems with my barostat, but I've been able to

isolate the problem to the constraint virial **.

Can anyone with experience programming a calculation of the constraint

virial (preferably in the context of Velocity-Verlet integration) please

reply to my private email so we can discuss the finer points of the

algorithm and hopefully resolve my dilemma?

Dzeinkuje,

Dave

** Proof of point:

- When I simulate an ideal gas, my barostat takes the system to the

correct volume given the applied external pressure (this means that the

kinetic energy term in the pressure calculation is correct).

- When I simulate a Lennard-Jones gas with a sizeable epsilon parameter,

my computed energies are in close agreement (1%) with AMBER and the

final system volume is within 0.3% of that obtained by AMBER. I think

there must still be some long-range correction running around that I can't

quite get rid of, but the essential result is that my code and AMBER

produce very similar final volumes for this gas system, and those final

volumes are a significant (12-fold decrease) departure from the volume of

a similar amount of an ideal gas. So, the non-bonded virial (at least in

the case of monatomic particles) is correct.

- When I simulate a system of TIP3P water molecules without using SETTLE

but rather a crude system of bonds between O-H1, O-H2, and H1-H2, the

system also reaches a reasonable and stable final volume, close to a

density of 1.0 g/cm3 (it is reasonable at this point to assume that any

deviation is a result of not making the molecules rigid). So, the

non-bonded virial, again, is correct, and I can simulate tri-atomic

molecules under NPT conditions without trouble.

- When I try to simulate TIP3P water (or any other three-site water) with

SETTLE for rigid molecules, the system blows up (slowly but exponentially,

it expands until a numerical catastrophe hits). My constraint virial is

therefore obviously the problem.

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

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

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

Received on Wed Feb 14 2007 - 06:07:37 PST

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