[gmx-users] (no subject)

Nilesh Dhumal 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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