Mark.Abraham at anu.edu.au
Thu May 18 10:15:21 CEST 2006
karamyog singh wrote:
> I exactly did that. I initially thought that since I have placed the
> atoms randomly so it is probable that atoms experience large forces and
> since I am not allowing any temperature scaling etc. , I am getting
> large KE. Therefore I first minimized my configuration. I got a frozen
> structure by doing pressure and temp. scaling. Then I removed
> everything. After that what happens is, the whole crystal starts
> breaking up. First one atom gains velocity and moves then another atom
> and then another. After tht the whole system just breaks.
Ah... your .mdp file generated velocities... you don't want to carefully
equilibrate something, and then put near-random numbers in place of the
velocities. You just want to turn off the regulation and set gen_vel = no.
> Any idea why? Is it because the no. of steps for my initial md run is
> small . Shall I stabilize my configuration for a longer time?
> The cut off that I have taken is the value of 'r' at which the minima
> for LJ exists. Is it ok or shall I increase this too?
This is certain to be too small. With correctly modeled LJ, you'd expect
to see a peak in the radial distribution function corresponding to that
minimum, since all the atoms will be jostling to get there with respect
to all other atoms - impossible of course, but they'll do it on average
for their closest neighbours. Here you won't necessarily see that,
because your effective potential function for all pairs of atoms drops
from infinity at zero distance to the distance of the minimum value, and
then to zero.
Elaborating, as soon as an atom moves to a distance greater than the
distance of the minimum, they don't interact. The other nearby
interactions will become more repulsive (if the gas is dense) and
effectively correct for it, but your effective potential function is not
LJ any more. Further you say your gas is dilute, so it seems unlikely
that you have a good physical model... atoms will collide, bounce past
the minimum distance and have no interactions with anything until they
collide with another atom. This is not true for an LJ system.
I'd say you want a cut-off such that the potential at that cutoff is
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