[gmx-users] inserting a new potential
Alan Wilter Sousa da Silva
alan at biof.ufrj.br
Thu Jul 24 19:09:01 CEST 2003
Thanks David Bostick,
I'll take a look abou acc-grps. Related to Forced Simulations?
Anyway, I want to disturb my systems. I do believe that gravitational
won't have any effect, but I would like to increase such field stepwise,
as much as necessary to see any result with a very interesting tool that
we have here for analysis.
On Thu, 24 Jul 2003, David L. Bostick wrote:
> Aren't directives in the mdp file called "acc_grps" and "accelerate" where
> you can give a constant acceleration to any set of atoms in the system?....
> That is, if you want to model gravity in the approximation that
> acceleration due to gravity is constant.
> If you want the classical 1/r^2
> force, I would imagine that you could rig the coulomb interaction to do
> this by giving fake charges to all the particles, provided you didn't want
> any of the atoms to be charged... that is..
> you don't want an electrostatic interaction AND a gravitational
> interaction. This sort of thing wouldn't make sense anyway, because
> gravity dominates on the large scale and electrostatics dominate on the
> small scale.
> David Bostick Office: 262 Venable Hall
> Dept. of Physics and Astronomy Phone: (919)962-0165
> Program in Molecular and Cellular Biophysics
> UNC-Chapel Hill
> CB #3255 Phillips Hall dbostick at physics.unc.edu
> Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
> On Thu, 24 Jul 2003, Alan Wilter Sousa da Silva wrote:
> > Hi List!
> > Despite what I've read in gmx manual 3.1.1 about defining a different
> > potential function (p. 122), I don't think it would serve to me. I would
> > like to insert a new force like gravitational field derived, i.e.,
> > unidirectional and acting over all atoms of simulation.
> > If I have to handle the code, from where should I have to start?
> > Any suggestion would be very welcome.
> > BTW, I'll do my homework looking at the code to get familiar.
> > Cheers,
> > --
> > -----------------------
> > Alan Wilter S. da Silva
> > -----------------------
> > Laboratório de Física Biológica
> > Instituto de Biofísica Carlos Chagas Filho
> > Universidade do Brasil/UFRJ
> > Rio de Janeiro, Brasil
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Alan Wilter S. da Silva
Laboratório de Física Biológica
Instituto de Biofísica Carlos Chagas Filho
Universidade do Brasil/UFRJ
Rio de Janeiro, Brasil
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