[gmx-users] bouncing molecules

[Derrick Guang Yuh Lee]

dear nuno

awhile back you responded to an e-mail posted on gromacs about how my
molecule moved from one side of my box, to the other. could you please
elaborate on what you meant by "periodic boundary conditions concept"?
thanks.


 - derrick



 derrick Lee
 faculty of Science
 Memorial University of Newfoundland
 k24dgyl at mun.ca or derrickglee at hotmail.com

"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
catalyst."
                                                              - bruce lee

On Fri, 28 Nov 2003, Nuno R. L. Ferreira wrote:

>
>
>
> > dear gmx-users
> >
> > i was just curious if someone could give me some insight to a particular
> > problem i am having. i have been working on a DPPC monolayer and just ran
> > a simulation for 1ns. when i look at it in VMD, it appears as if one or
> > two of the DPPC lipids all of a sudden bounce from one edge of my box, to
> > the opposite end.
>
> periodic boundary conditions concept
>
> >
> > the only conclusion i can come up w/ is that the box is too small and the
> > lipid is being cut and sent to the opposite side for some reason. if
> > there is another reason, please inform me, and of any possible ways to
> > fix this. thanks.
> >
> >
> >  - derrick
> >
> >
> >
> >  derrick Lee
> >  faculty of Science
> >  Memorial University of Newfoundland
> >  k24dgyl at mun.ca or derrickglee at hotmail.com
> >
> > "a teacher is never a giver of truth - he is a guide, a pointer to the
> > truth that each student must find for himself. a good teacher is merely a
> > catalyst."
> >                                                               - bruce lee
> >
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