[gmx-users] (no subject)
ndhumal at andrew.cmu.edu
Thu Apr 19 21:18:13 CEST 2012
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.
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