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 <hmkv...@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 > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
