On 17/05/2012 11:48 AM, kevin wrote:
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.
Unfortunately the development of GROMACS is not fast enough to suit
anybody's wishes, and too fast and complex to make it worth people's
volunteer time to do much beyond what can be observed by inspecting the
code. I suggest you step through a run of GROMACS with your favourite
debugger on a similar calculation and observe the control flow.
There is some discussion of data structures on the GROMACS webpage which
is more-or-less useful for the 4.0/4.5 series.
Mark
------------------------------------------------------------------------
kevin.len
*From:* Mark Abraham <mailto:mark.abra...@anu.edu.au>
*Date:* 2012-05-16 13:57
*To:* Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>
*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 <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.
Mark
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