Hello, I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules.
I am running simulation for two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE charge=-1 : Charge on solute For second case I am using rerun option to calculate the energy with charge for same configuration. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o md-rerun.tpr /opt/mpich_intel/ch-p4/bin/mpirun -machinefile cp -np 2 /usr/local/gromacs/bin/mdrun_mpi -s md-rerun.tpr -o md-rerun.trr -c solvent-bmi-pf6-128.pdb -e md-rerun.edr -rerun md.trr -g md-rerun.log The total energy difference between change and neutal is large around ~350 kj/mole. It should be around 30 kJ /mole. Can you tell why I getting large high energy differmece. I using Gromacs VERSION 4.0.5. NIlesh -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
