<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span><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></span></div><div><br></div><div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><font size="2" face="Arial"><hr size="1"><b><span style="font-weight:bold;">From:</span></b> Sanku M <msanku65@yahoo.com><br><b><span style="font-weight: bold;">To:</span></b> Dommert Florian <dommert@icp.uni-stuttgart.de><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></font><br><div id="yiv134867621"><div style="color: rgb(0, 0, 0); background-color: 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><div style="font-size: 12pt; font-family: times, serif; "><div style="font-size: 12pt; font-family: times, serif; "><font size="2" face="Arial"><hr size="1"><b><span style="font-weight:bold;">From:</span></b> Dommert Florian
<dommert@icp.uni-stuttgart.de><br><b><span style="font-weight:bold;">To:</span></b> Sanku M <msanku65@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org><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>> gmx-users mailing list <a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a rel="nofollow" target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a rel="nofollow" target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to <a rel="nofollow" ymailto="mailto:gmx-users-request@gromacs.org" target="_blank" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a rel="nofollow" target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br><br><br>-- <br>Florian Dommert<br>Dipl. - Phys.<br><br>Institute for Computational Physics<br>University
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