[gmx-users] bouncing molecules

Nuno R. L. Ferreira nunolf at ci.uc.pt
Fri Nov 28 15:15:04 CET 2003

> 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
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list