[gmx-users] freezing grps during em

Dear Users, Sorry for maybe naive question. I am new user of gmx. I like to fix the positions of three atoms in three neighboring residues (not connected) with respect to each other. These atoms are very close to each others and van der waals interaction makes the distance larger after em. Howe

[gmx-users] making movie from trajectories

Dear All, I would like to make a movie from my trajectories using vmd. I need to make a movie which during the simulation the color of model is changing after some frames during the dynamics (showing the transition between two states), this is accompanied by showing the change in time clock and