[gmx-users] how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box

Dear All, This has been discussed before for individual frames. But I am having a problem in trying to center a trajectory so that the bilayer remains at the center of the box. I have tried several combinations, but none of the them work. In each case, the centering and/or the fitting is done on

Re: [gmx-users] how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box

What is the problem exactly? The two layers separate over the pbc? did you try a -pbc nojump prior the centering? On Jul 3, 2009, at 11:37 AM, maria goranovic wrote: Dear All, This has been discussed before for individual frames. But I am having a problem in trying to center a trajectory