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
topology.
-Justin
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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