[gmx-users] msd vs. time plot for molecules

Using g_msd on a group of atoms results in an msd vs. time plot which is the result of an average over all the atoms' motions. I would like to obtain the same plot, but for an average over the center of mass motions of a group of molecules. Using the -mol option results in a plot of the

[gmx-users] DPPC bilayer simulation crash

I am trying to perform a simulation of 128 dppc in 3655 spc water. I obtained .pdb and .top files from the Biocomputing website at U.Calgary. I do nothing to alter the structure, which must be minimized as it comes from the end of a 1 ns simulation. Processing the input files works fine, but