[gmx-users] (no subject)

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 21 16:24:09 CEST 2010

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.


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