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    On 17/05/2012 11:48 AM, kevin wrote:
    <blockquote cite="mid:tencent_18E34A920E47834C44C5B43A@qq.com"
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      <div><includetail><br>
          &nbsp;</includetail></div>
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          <div>Thanks.&nbsp;&nbsp;I think I should&nbsp;have&nbsp;a&nbsp;look&nbsp;at some specific
            documents to&nbsp;understand&nbsp;the&nbsp;flow&nbsp;of&nbsp;control.</div>
          <div>
            <div>Namely, to understand what is purpose of the
              subroutines in&nbsp;src/mdlib/.&nbsp; 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>
    <br>
    <blockquote cite="mid:tencent_18E34A920E47834C44C5B43A@qq.com"
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            <div>&nbsp;</div>
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          <div>&nbsp;</div>
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          <div><span>kevin.len</span></div>
          <div>&nbsp;</div>
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              <div><b>From:</b>&nbsp;<a moz-do-not-send="true"
                  href="mailto:Mark.Abraham@anu.edu.au">Mark Abraham</a></div>
              <div><b>Date:</b>&nbsp;2012-05-16&nbsp;13:57</div>
              <div><b>To:</b>&nbsp;<a moz-do-not-send="true"
                  href="mailto:gmx-users@gromacs.org">Discussion list
                  for GROMACS users</a></div>
              <div><b>Subject:</b>&nbsp;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:
              <blockquote
                cite="mid:tencent_7305DC70170F43AD1985462C@qq.com"
                type="cite">
                <div>
                  <div>&nbsp;Hi, everyone.</div>
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                        <div class="FoxDiv20120516095726296235">
                          <div>&nbsp;</div>
                          <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&nbsp;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>.&nbsp; </span></span><span
                              class="subtitle"><span dir="ltr">I see
                                there is an algorithm called "SHAKE" or
                                "RATTLE "which and it seems&nbsp;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>
                          <div>
                            <div><span class="subtitle"><span dir="ltr"></span></span><br>
                            </div>
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              </blockquote>
              <br>
              Various files in src/mdlib/ deal with these kinds of
              algorithms.<br>
              <br>
              Mark<br>
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