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@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-requ...@gromacs.org. Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > > -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
