CCL: Question regarding availability of a simulation code
- From: Josh BERRYMAN <Josh.Berryman(-)uni.lu>
- Subject: CCL: Question regarding availability of a simulation
code
- Date: Mon, 9 Nov 2015 06:47:31 +0000
Sent to CCL by: Josh BERRYMAN [Josh.Berryman]-[uni.lu]
The normal definition of hard spheres is as an infinite potential stepping
instantly down to zero at r=.5. That is not compatible with defining forces
usefully, so HS simulations are done with event-driven MD rather than the normal
fixed-timestep methods. Marcus Bannerman et al.'s DynamO is an open-source
event-driven HS code.
The best mixing of ED simulations with a continuous potential such as the
Coulomb force is not obvious. One approach is to discretise the Coulomb
potential, and treat level crossings as a special type of collision. Another
approach might be to run fixed-timestep MD with EDMD taking place in between the
fixed timesteps.
For lengthscales where the HS potential is meaningful (micrometres and up) you
might find that you are in low Reynolds-number-land, in which case it is
probably quite OK to use a Brownian Dynamics approximation: you can evolve the
system using Monte Carlo in this case, with small fixed-size steps in space,
thus avoiding the need to define forces. Code for this approach is extremely
simple, most groups just write their own see eg. Frenkel & Smit's book, or
Allen & Tildesley, both of which have code recipies. Allen & Tildesley
is free online as far as I can remember.
Josh
________________________________________
> From: owner-chemistry+josh.berryman==uni.lu(0)ccl.net
[owner-chemistry+josh.berryman==uni.lu(0)ccl.net] on behalf of Susi Lehtola
susi.lehtolaa/alumni.helsinki.fi [owner-chemistry(0)ccl.net]
Sent: Sunday, November 08, 2015 05:06 PM
To: Josh BERRYMAN
Subject: CCL: Question regarding availability of a simulation code
Sent to CCL by: Susi Lehtola [susi.lehtola\a/alumni.helsinki.fi]
On 11/06/2015 10:04 PM, Rakesh Srivastava allahabad.21::gmail.com wrote:
> Dear scholars,
> I want to know, is there any MD code available which can simulate a
> system of spherical particles which interact via hard sphere and
> electrostatic potential.
> Thanks in advance.
For instance GROMACS (http://www.gromacs.org) can do this, you'd just
probably have to use a tabulated potential for your calculation. There
was some discussion on the mailing list a few years ago
http://comments.gmane.org/gmane.science.biology.gromacs.user/36201
--
-----------------------------------------------------------------------
Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow
susi.lehtola+/-alumni.helsinki.fi Lawrence Berkeley National Laboratory
http://www.helsinki.fi/~jzlehtol USA
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