[gmx-users] Re: Dimer jumping during simulation

Kavyashree M hmkvsri at gmail.com
Sat Dec 1 23:41:05 CET 2012

Dear users,

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


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

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