On 22/10/2010 1:17 AM, Nilesh Dhumal wrote:
I am doing solvation dynamics for my system.
I have system with diatomic (PA---NE)solute surrounded by water molecules.
I want to run simulation with 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
I want to calculate the energy at each step keeping the solvent
configration same.
IF I start a simulation with no charge on solute (case1), I have the
energy for 1 step. I want to calculate the energy with charge on solute
(case 2) with same configration water molecules.
Each step I want to calculate the energy with and without charge on
solute since the configration of solvent will be same for that step.
I was thinking two make two topologies file with charge and with out
charge on solute. I don't know how to use them simultaneously during the
simulation.
Well, you don't use them simultaneously. You run a simulation on
whatever you think will generate a relevant conformational ensemble.
Then you want to use mdrun -rerun twice on the resulting trajectory,
using .tpr files based on .top files corresponding to the two cases in
order to create your comparison.
Mark
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