[gmx-users] Spherical shaped box

Dear users,   I am doing Protein Ligand simulation, increasing temp. from 100, 200, to 300 K. after 1ns of simulation in 300 K, the protein jumps out of the box and when I use the command    trjconv_mpi  -f *.trr -s *.tpr -o *new.trr -pbc nojump   followed by     trjconv_mpi -f  new*.trr -s

Re: [gmx-users] Spherical shaped box

Hi Sogol, You remove jumps over periodic boundary conditions, giving a continuous trajectory. That gives you a very nice view on diffusion in your system, which happens to be equal in all directions. Hence, the end result looks spherical. But that's not the same as having a spherical box. If you

Re: [gmx-users] Spherical shaped box

Dear Tsjerk   Thank you   Sogol From: Tsjerk Wassenaar tsje...@gmail.com To: Kowsar Bagherzadeh kw_bagherza...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, May 16, 2012 2:46 PM Subject: Re: [gmx-users] Spherical shaped