[gmx-users] (no subject)

Nilesh Dhumal ndhumal at andrew.cmu.edu
Tue Oct 26 01:49:58 CEST 2010

I run a test simulation for -rerun. I didn't change the topology file.

grompp -f md.mdp  -c  solvent-bmi-pf6-128.pdb  -p  solvent-bmi-pf6-128.top
 -o 3.tpr
mpirun -machinefile cp -np 8 mdrun -s 3.tpr -o 3.trr   -c
solvent-bmi-pf6-128.pdb -e 3.edr -g 3.log

with -rerun
grompp -f md.mdp  -c  solvent-bmi-pf6-128.pdb  -p  solvent-bmi-pf6-128.top
 -o 6.tpr
mpirun -machinefile cp -np 8 mdrun -s 6.tpr -o 6.trr -rerun 3.trr  -c
solvent-bmi-pf6-128.pdb -e 6.edr -g 6.log

I calculate the total energy by
g_energy -f 3.edr -o 3.xvg
g_energy -f 6.edr -o 6.xvg

The total energy varies between +- 30.00 KJ/mol.
It should be constant since I using same topology file and trajectory.
Why the total energy is not constant.

On Thu, October 21, 2010 10:24 am, Mark Abraham wrote:
> On 22/10/2010 1:17 AM, 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.
> Well, you don't use them simultaneously. You run a simulation on
> whatever you think will generate a relevant conformational ensemble. Then
> you want to use mdrun -rerun twice on the resulting trajectory, using .tpr
> files based on .top files corresponding to the two cases in order to
> create your comparison.
> Mark
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