[gmx-users] Re: Dimer jumping during simulation

[Kavyashree M]

Dear users,

I used -center along with -pbc mol selecting protein for both options
Its fine now both monomers are in the box.

Thanks
kavya

On Sun, Dec 2, 2012 at 1:47 AM, Kavyashree M <hmkvsri at gmail.com> wrote:

> Dear users,
>
> I have simulated a protein dimer using OPLS-AA in 4.5.3 version.
> Analysing simulation showed that one of the monomer is out side
> the box.
> I tried trjconv pbc -nojump and trjconv -pbc mol
> still some fraction of a time one of them goes out. Can anyone
> suggest some solution to this.
> I need to calculate the radius of gyration of dimer, this value differs
> when i use treated and untreated trajectories.
> So Kindly suggest some solution.
>
> Thank you
> kavya
>