[gmx-users] (no subject)

Nilesh Dhumal ndhumal at andrew.cmu.edu
Thu Oct 21 16:17:13 CEST 2010

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


On Thu, October 21, 2010 10:03 am, Mark Abraham wrote:
> On 21/10/2010 11:55 PM, Nilesh Dhumal wrote:
>> Hello,
>> I am working on a system which has a diatomic solute surrounded by water
>>  molecules. I want to calculate the energy for each step with and with
>> out charge on solute simultaneously. Pl. help me solve this problem.
> I don't understand what you want to do.
> Mark
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