On 26/09/2011 11:59 PM, Sanku M wrote:
I did not mean lattice boltzmann by BD.
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.

The manual section of BD doesn't mention it, so very probably not.

Mark


------------------------------------------------------------------------
*From:* Sanku M <msank...@yahoo.com>
*To:* Dommert Florian <domm...@icp.uni-stuttgart.de>
*Sent:* Monday, September 26, 2011 6:07 AM
*Subject:* Re: [gmx-users] BD with Hydrodynamic interactions?

I did not mean lattice boltzmann by BD.
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.

------------------------------------------------------------------------
*From:* Dommert Florian <domm...@icp.uni-stuttgart.de>
*To:* Sanku M <msank...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org>
*Sent:* Monday, September 26, 2011 3:38 AM
*Subject:* Re: [gmx-users] BD with Hydrodynamic interactions?

On Sun, 2011-09-25 at 14:03 -0700, Sanku M wrote:
> Hi,
>  I was wondering whether BD simulation integrator in Gromacs also
> have option of including hydrodynamic interactions.

Hello,

I do not think, that Gromacs has something like Lattice-Boltzmann
implemented so far. Furthermore you would need a momentum-conserving
method for the calculation of the electrostatic forces, which is not
given with the analytical differentiation of SPME, that conserves only
energy and not momentum.

/Flo

> Sanku
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--
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

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