From owner-chemistry: at :ccl.net Mon Nov 9 07:58:01 2015 From: "Josh BERRYMAN Josh.Berryman*_*uni.lu" To: CCL Subject: CCL: Question regarding availability of a simulation code Message-Id: <-51868-151109014739-30713-JuMsLzIQO7kCrmgHFaxzNA . server.ccl.net> X-Original-From: Josh BERRYMAN Content-Language: en-JM Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 9 Nov 2015 06:47:31 +0000 MIME-Version: 1.0 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 -----------------------------------------------------------------------http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt