[gmx-users] bouncing molecules

[Nuno R. L. Ferreira]

Hi Derrick

Please check gmx manual at page 11.
Shortly, its a clever computational trick , in order to mimic the presence
of an infinite bulk surrounding our N-particle model system.

Regards,
NUno

P.S. If you want to see the trajectory in VMD without those molecules moving
from one side of the box to the other,  you can use trjconv and the
flags -pbc and -ur. Check gmx e-mail list, think this issue was already
asked by someone.

----- Original Message ----- 
From: "Derrick Guang Yuh Lee" <k24dgyl at mun.ca>
To: <gmx-users at gromacs.org>
Sent: Monday, December 22, 2003 4:39 PM
Subject: Re: [gmx-users] bouncing molecules


> 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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