[gmx-users] Energy cal from MD simulations

Hi, I have obtained a 100 ns simulation using Amber. I would like to calculate the potential energy (VDW, COUL,ect) from the trajectory, below is my command. $gmx grompp -f test.mdp -p ../gromacs.top -n ../index.ndx -c ../300.pdb -o rerun.tpr -maxwarn 1 $gmx mdrun -rerun ../protein.trr -s rerun.

[gmx-users] Gromacs-fda

Hi amber users I am trying to analyze protein pairwise-forces for my protein. After getting some files and running the following commands: $ gmx_fda editconf -f 300.pdb -o pdb.gro $ gmx_fda grompp -f test.mdp -c pdb.gro -p gromacs.top -o water.tpr -maxwarn 5 $ gmx_fda make_ndx -f water.tpr $ gmx_