[gmx-users] (no subject)

[Nilesh Dhumal]

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