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

kevin kevin.len at foxmail.com
Thu May 17 03:48:10 CEST 2012

Thanks.  I think I should have a look at some specific documents to understand the flow of control.
  Namely, to understand what is purpose of the subroutines in src/mdlib/.  But I could not find such
 information in the Gromacs user manual. Do anyone know such an document? Thanks.

   From: Mark Abraham
 Date: 2012-05-16 13:57
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks.

  On 16/05/2012 12:28 PM, kevin wrote:     Hi, everyone.
 It is my first use of Gromacs 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.  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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