Is there any bug in rerun option?
Nilesh
On Mon, October 25, 2010 8:50 pm, Mark Abraham wrote:
----- Original Message -----
From: Nilesh Dhumal<ndhu...@andrew.cmu.edu>
Date: Tuesday, October 26, 2010 10:50
Subject: Re: [gmx-users] (no subject)
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
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.
Those .tpr should be identical - but you can check that with
gmxcheck.> Reruns do neighbour-searching every step, whereas your normal
simulation
followed the nstlist setting. That's part of why my earlier advice
suggested doing reruns for each simulation you wish to
compare. You
should be able to get good/better agreement for steps where nstlist
directed neighbour-searching in the original run. Also,
whether or not
constraints have been applied (and when!) could influence the
energies to
about this degree. I don't recall the details here.
Even once you've removed all algorithm-specific sources of
difference,> there are other sources of non-reproducibility, such as the
assignment of
particles to DD cells. Your original mdrun probably used dynamic
load-balancing, and that cannot be reproduced in the DD used
by the
rerun. (Or indeed by a repeat of your original mdrun!) Setting
-dlb no in
the original simulation might be enough to get agreement here,
or maybe
mdrun -reprod will be required.
Mark
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
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