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

I remember having a similar issue a long time ago. If I remember correctly, the culprit was a bad parametrization of the Langevin piston. Maybe you should specified how the pressure is controlled, as well as how you managed the center of mass motions in you dynamics. Nicolas > Well the bilayer d

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

This sounds pretty bad! You have a drift of your all system apparently ... Did you not remove the COM of your system? For membranes it is often recommended to remove the water and the lipid bilayer separately. The might drift one from the other. On Jul 3, 2009, at 12:19 PM, maria goranovic wr

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

Well the bilayer drifts down in the z-direction, and eventually the leaflets almost separate, with each leaflet being on opposite ends of the box. if i try pbc nojump, the lipids drift far away from the box in the xy plane On Fri, Jul 3, 2009 at 12:00 PM, wrote: > Send gmx-users mailing list s