[gmx-users] (no subject)

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 21 16:21:36 CEST 2010

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.

You can't.  Probably the best option is to do an mdrun -rerun using the second 


> 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
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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