[gmx-users] (no subject)

[Nilesh Dhumal]

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.

NIlesh

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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org. Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
>
>
>