[gmx-users] question about energy minimization

Amit Choubey kgp.amit at gmail.com
Tue Sep 29 21:36:19 CEST 2009

Hi Omer,

My question was to how to avoid the "diffusion" of molecules out of the box
during energy minimization and MD  run? I think what you suggested here will
just change the present trajectory into a new by using the pbc condition.

But i am wondering shouldnt this be done in MD calculation itself. It seems
me to me that physics will be significantly different if i dont put the
particles which go out of the box, back into the box. In that way the box
will keep on expanding as i increase my simulation time and the calculated
equilibirium properties wont be very meaningful and will fluctuate more than
they really should.

By the way i am talking about long chain lipid molecules here and i am using
an all bond constraint.


On Tue, Sep 29, 2009 at 5:17 AM, Omer Markovitch <omermar at gmail.com> wrote:

> Trj "trjconv -pbc nojump", or "trjconv -h" and read the short help printed.
> Omer.
>> I actually didnt realize this until i did a long simulation after which
>> the trajectories of some of the atoms looked way out of the box dimensions.
>> The co-ordinates of many atoms didnt lie in the box range. Although the
>> output file contained the same box dimensions as I started with. Could
>> someone help me in understanding what happened?
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