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On 17/05/2012 11:48 AM, kevin wrote:
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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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<br>
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.<br>
<br>
There is some discussion of data structures on the GROMACS webpage
which is more-or-less useful for the 4.0/4.5 series.<br>
<br>
Mark<br>
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<div><span>kevin.len</span></div>
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<div><b>From:</b> <a moz-do-not-send="true"
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 moz-do-not-send="true"
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>
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<div class="FoxDiv20120517093246140547">On 16/05/2012 12:28
PM, kevin wrote:
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cite="mid:tencent_7305DC70170F43AD1985462C@qq.com"
type="cite">
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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>
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<br>
Various files in src/mdlib/ deal with these kinds of
algorithms.<br>
<br>
Mark<br>
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