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