[gmx-users] Fatal error: atoms 970 and 973 in charge group 600 are in different energy groups

Dear colleague, I want to calculate the Coul-SR energy and LJ energy between the receptor and PART of my ligand, using a given XTC file with "mdrun -rerun". I modified "energygrps" in the MDP file, and then type grompp -f md_rerun.mdp -c pr_out.gro -p receptor.top -n index.ndx -o rerun.tpr He

[gmx-users] May I use "-b" and "-e" in the cosine con tent calculation of PC?

Hi dear friends,   I just made an essential dynamics of 5ns; I calculated the cosine content of PC1 by using g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg it gave: "Cosine content of set 1 with 0.5 periods: 0.749969" the value is rather too high.   However, I found that only trajectory between 3300