[gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks.

Mark Abraham Mark.Abraham at anu.edu.au
Wed May 16 07:57:48 CEST 2012

On 16/05/2012 12:28 PM, kevin wrote:
>  Hi, everyone.
> It is my first use of Gromacs <http://lammps.sandia.gov/> and I am 
> looking for a numerical scheme for one specific constrained SDE, the 
> constrain is a macroscopic one, i.e., overdamped Langevin(Brownian 
> dynamics) equations with an equality constraint which is expressed in 
> form of expectation(or moment of n-th order). This is unlike the 
> common 'micro' constraint(simply function in terms of variable in SDE) 
> . I can not find such a subrountine for solving constrained SDE in MD 
> codes in Gromacs <http://lammps.sandia.gov/>. I see there is an 
> algorithm called "SHAKE" or "RATTLE "which and it seems they could 
> implement Langevin(or Brownian) dynamics with constraints. If 
> convenient, could anyone help to point out which subroutine is 
> specific for implementing SHAKE/RATTLE? Thanks in advance.

Various files in src/mdlib/ deal with these kinds of algorithms.

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