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<DIV>Thanks. I think I should have a look at some specific documents to understand the flow of control.</DIV>
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<DIV>Namely, to understand what is purpose of the subroutines in src/mdlib/. But I could not find such</DIV>
<DIV>information in the Gromacs user manual. Do anyone know such an document? Thanks.</DIV>
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<DIV><SPAN>kevin.len</SPAN></DIV>
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<DIV><B>From:</B> <A href="mailto:Mark.Abraham@anu.edu.au">Mark Abraham</A></DIV>
<DIV><B>Date:</B> 2012-05-16 13:57</DIV>
<DIV><B>To:</B> <A href="mailto:gmx-users@gromacs.org">Discussion list for GROMACS users</A></DIV>
<DIV><B>Subject:</B> Re: [gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks.</DIV></DIV></DIV>
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<DIV class=FoxDiv20120517093246140547>On 16/05/2012 12:28 PM, kevin wrote:
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<DIV> Hi, everyone.</DIV>
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<DIV>It is my first use of <A href="http://lammps.sandia.gov/" moz-do-not-send="true">Gromacs</A> and I am looking for a numerical scheme for one specific constrained SDE, the constrain <SPAN class=subtitle><SPAN dir=ltr>is a macroscopic one, i.e., overdamped Langevin(Brownian dynamics) equations with an equality constraint which is </SPAN></SPAN><SPAN class=subtitle><SPAN dir=ltr>expressed in form of expectation(or moment of n-th order). </SPAN></SPAN><SPAN class=subtitle><SPAN dir=ltr>This is unlike the common 'micro' constraint(simply </SPAN></SPAN><SPAN class=subtitle><SPAN dir=ltr>function in terms of variable in SDE) . I can not find such a subrountine </SPAN></SPAN><SPAN class=subtitle><SPAN dir=ltr>for solving constrained SDE in </SPAN></SPAN><SPAN class=subtitle><SPAN dir=ltr>MD codes in <A href="http://lammps.sandia.gov/" moz-do-not-send="true">Gromacs</A>. </SPAN></SPAN><SPAN class=subtitle><SPAN dir=ltr>I see there is an algorithm called "SHAKE" or "RATTLE "which and it seems they could </SPAN></SPAN><SPAN class=subtitle><SPAN dir=ltr>implement Langevin(or Brownian) dynamics with constraints. If convenient, could anyone help to point out which subroutine </SPAN></SPAN><SPAN class=subtitle><SPAN dir=ltr>is specific for implementing SHAKE/RATTLE? Thanks in advance.</SPAN></SPAN></DIV>
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<DIV><SPAN class=subtitle><SPAN dir=ltr></SPAN></SPAN><BR></DIV></DIV></DIV></DIV></DIV></DIV></DIV></BLOCKQUOTE><BR>Various files in src/mdlib/ deal with these kinds of algorithms.<BR><BR>Mark<BR></DIV></DIV></DIV></includetail></DIV>