[gmx-users] Regarding PBC

[Mark Abraham]

Hi,

You can start at
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark

On Sun, Apr 2, 2017 at 9:39 PM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> Hello,
>
> I ran a energy minimization followed by nvt, npt, md simulation...and
> during analysis, if i look my .gro file  structure in vmd and i write in
> tkconsole as pbc box and see that *some  of the molecules are not inside
> the box, they have been outside the box*, is there anything wrong..?? how
> can i knw about this..?? any  influence of PBC....etc.,
>
> how can i clear all these doubts..?? is there any prescribed
> book/references for it...thn it would help a lot...
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
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