[gmx-users] Dimer jumping during simulation

Kavyashree M hmkvsri at gmail.com
Sat Dec 1 21:17:29 CET 2012

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

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