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On 16/05/2012 12:28 PM, kevin wrote:
<blockquote 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 moz-do-not-send="true"
href="http://lammps.sandia.gov/">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
moz-do-not-send="true"
href="http://lammps.sandia.gov/">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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</blockquote>
<br>
Various files in src/mdlib/ deal with these kinds of algorithms.<br>
<br>
Mark<br>
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