AMBER Archive (2001)

Subject: shake comparison

From: Xiaoliang Qian (qian_at_biomath.nyu.edu)
Date: Fri Feb 23 2001 - 11:13:07 CST

Hi, everyone.

I have a question about the shake schemes in Charmm and AMBER.
I found two shake schemes exist

X0: coordinate at t0,
X1: coordinate at t0+dt, before shake correction
X2: coordinate at t0+dt, after shake correction
V0: velocity at t0;
V1: velocity at t0+dt, with shake correction;

X1=X0+V0*dt
X2=X1+SHKDIFF(X0,X1)
V1=(X2-X0)/dt -------------------- scheme I
or
V1=V0+(X2-X1)/dt ------------------ scheme II

Scheme I is used for single time step integrator
both in Charmm and AMBER.

Scheme II is used for multi-time step integrator in Charmm.

Can anyone explain to me why different shake schemes are used?

Xiaoliang