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

Mark Abraham Mark.Abraham at anu.edu.au
Fri May 18 08:36:09 CEST 2012

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.


> ------------------------------------------------------------------------
> kevin.len
> *From:* Mark Abraham <mailto:Mark.Abraham at anu.edu.au>
> *Date:* 2012-05-16 13:57
> *To:* Discussion list for GROMACS users <mailto:gmx-users at 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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