[gmx-users] [OT] Software package for discontinuous molecular dynamics? (DMD)

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 3 08:58:54 CET 2010

On 2/2/10 10:53 PM, ms wrote:
> David van der Spoel ha scritto:
>> On 2/2/10 4:43 PM, ms wrote:
>>> David van der Spoel ha scritto:
>>>> On 2/1/10 4:32 PM, ms wrote:
>>>>> Hi,
>>>>> Sorry for the offtopic but Google/literature quick search is not
>>>>> helping
>>>>> and I'd like to have some more informed opinion.
>>>>> To my understanding, GROMACS isn't capable of discontinuous molecular
>>>>> dynamics. Is there any more-or-less standard software package for that?
>>>>> thank you!
>>>>> m.
>>>> Can you be more specific please?
>>> Uhm, in what meaning?
>>> I was pondering about using DMD for use with a coarse-grained model and
>>> I wondered if there is a standard package for that. Don't know how to be
>>> more specific, what is unclear in my question?
>>> thanks,
>>> M.
>> What is discrete MD?
> Uh, sorry. Probably references know better than me:
> http://pubs.acs.org/doi/full/10.1021/ja0539140 is an example of it
> applied to proteins. (I am looking for reviews on the subject but can't
> find recent ones) It is a coarse-grained technique for use with
> discontinuous potentials, which roughly speaking uses "collision
> detection" instead of fine-grained potential calculation:
> "In a discontinuous molecular dynamics (DMD) simulation, particles
> collide when they arrive at a discontinuity in the potential, that is,
> the hard-sphere diameter or the square-well width. Between collisions,
> particles move with linear trajectories, making DMD simulations much
> faster than traditional molecular dynamics simulations with continuous
> potentials which require a small integration time step. The
> postcollision velocities of particles in DMD are found by solving the
> collision dynamics equations analytically."
> (from http://pubs.acs.org/doi/full/10.1021/la049267s )
> I don't know much about it, but I was curious and I wanted to know if
> there was a package for it (or if Gromacs was capable of it).
> thanks!
> m.
I see, in hindsight I had heard of it on a recent conference. Out of the 
box this will not work in Gromacs. How much work it would be to 
implement I don't know either, and since you lose the advantage Gromacs 
has on fast evaluation of the forces, you may be better off with another 

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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