**From:** Siddharth (*sshrinivasan_at_gmail.com*)

**Date:** Mon Oct 01 2007 - 17:02:11 CDT

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Hi

I have an implementation specific question regarding the

implementation of the SETTLE algorithm in NAMD. Peter Kollman's

original paper details the SETTLE algorithm, where the positional

constraints are implemented using a "reference triangle" approach and

the velocity constraints are implemented by subtracting off the

component of velocity along the O-H bonds. I noticed in NAMD, the

positional constraints are implemented exactly like the paper

suggests (settle1 () in Settle.c), and the velocity constraints are

also implemented like the paper (settle2 () in Settle.c). However the

velocity constraint routine never seem to be actually called, even

though the code exists. The half-step velocities are constrained in

the settle1 () routine, presumably for the VV integrator by taking

the difference between the constrained position and the original

position and dividing by the timestep. Logically it makes sense to

update the velocities just once, either at the half-step stage (t+dt/

2) or at the full-step stage (t+dt). I am wondering if someone can

1. Tell me if my interpretation of the source is correct. And if it

is wrong, where the settle2 ()/rattle2 () routine is actually being

called

2. Explain the reasoning behind this deviation from the original

paper, where only half step velocities need adjusting

I apologize if my question is on the wrong forum, but its my first

time using the group.

Thanks,

Sid

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