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

ms devicerandom at gmail.com
Tue Feb 2 22:53:31 CET 2010

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).


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