[gmx-users] pull code yields non-zero separations at t=0

Using gromacs 3.3.1: I am currently trying to using the pull code to do non-equilibrium simulations that will remove a ligand from a binding pocket in a directionally unbiased manner. As far as I can tell, some type of harmonic distance restraint is not possible using center of mass that has a

[gmx-users] pull code yields non-zero separations at t=0

My appologies, I wasn't doing mass weighting to determine the initial offset. It works perfectly with a loop like this in g_com.c: clear_rvec(coms); coms_count=0.0; for(i=0; inidx; i++){ coms[XX]+=fr.x[index[i]][XX]*top.atoms.atom[index[i]].m;