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On 26/09/2011 11:59 PM, Sanku M wrote:
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<div><span>I did not mean lattice boltzmann by BD.</span></div>
<div><span> By BD I meant Brownian Dynamics. In general, for
accuracy in dynamics, one uses hydrodynamic interaction
in brownian dynamics simulation. I was wondering whether
hydrodynamic interaction is invoked in gromacs
implementation of brownian dynamics simulation.</span></div>
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<br>
The manual section of BD doesn't mention it, so very probably not.<br>
<br>
Mark<br>
<br>
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<hr size="1"><b><span style="font-weight:bold;">From:</span></b>
Sanku M <a class="moz-txt-link-rfc2396E" href="mailto:msanku65@yahoo.com"><msanku65@yahoo.com></a><br>
<b><span style="font-weight: bold;">To:</span></b> Dommert
Florian <a class="moz-txt-link-rfc2396E" href="mailto:dommert@icp.uni-stuttgart.de"><dommert@icp.uni-stuttgart.de></a><br>
<b><span style="font-weight: bold;">Sent:</span></b>
Monday, September 26, 2011 6:07 AM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] BD with Hydrodynamic interactions?<br>
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rgb(255, 255, 255); font-size: 12pt; font-family: 'times
new roman', 'new york', times, serif; ">
<div><span>I did not mean lattice boltzmann by BD.</span></div>
<div><span> By BD I meant Brownian Dynamics. In general,
for accuracy in dynamics, one uses hydrodynamic
interaction in brownian dynamics simulation. I was
wondering whether hydrodynamic interaction is
invoked in gromacs implementation of brownian
dynamics simulation.</span></div>
<div><br>
</div>
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">
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<hr size="1"><b><span style="font-weight:bold;">From:</span></b>
Dommert Florian
<a class="moz-txt-link-rfc2396E" href="mailto:dommert@icp.uni-stuttgart.de"><dommert@icp.uni-stuttgart.de></a><br>
<b><span style="font-weight:bold;">To:</span></b>
Sanku M <a class="moz-txt-link-rfc2396E" href="mailto:msanku65@yahoo.com"><msanku65@yahoo.com></a>; Discussion
list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
<b><span style="font-weight:bold;">Sent:</span></b>
Monday, September 26, 2011 3:38 AM<br>
<b><span style="font-weight:bold;">Subject:</span></b>
Re: [gmx-users] BD with Hydrodynamic interactions?<br>
</font><br>
On Sun, 2011-09-25 at 14:03 -0700, Sanku M wrote: <br>
> Hi,<br>
> I was wondering whether BD simulation
integrator in Gromacs also<br>
> have option of including hydrodynamic
interactions.<br>
<br>
Hello,<br>
<br>
I do not think, that Gromacs has something like
Lattice-Boltzmann<br>
implemented so far. Furthermore you would need a
momentum-conserving<br>
method for the calculation of the electrostatic
forces, which is not<br>
given with the analytical differentiation of SPME,
that conserves only<br>
energy and not momentum.<br>
<br>
/Flo<br>
<br>
> Sanku<br>
> -- <br>
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<br>
-- <br>
Florian Dommert<br>
Dipl. - Phys.<br>
<br>
Institute for Computational Physics<br>
University Stuttgart<br>
<br>
Pfaffenwaldring 27<br>
70569 Stuttgart<br>
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Tel.: +49 - (0)711 - 68563613<br>
Fax.: +49 - (0)711 - 68563658<br>
<br>
<br>
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