[gmx-users] (no subject)

[Nilesh Dhumal]

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
rm -f *#*

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

The total enregy vaies beteen +- 30.00 KJ/mol.
It should be constant since I using same topology file and trajectroy.
Why the total energy is not contant.
NIlesh




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
> --
> 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
>
>
>