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.
kevin.len
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.
Mark--
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