[gmx-users] (no subject)

[Mark Abraham]

----- Original Message -----
From: Nilesh Dhumal <ndhumal at andrew.cmu.edu>
Date: Wednesday, October 27, 2010 1:04
Subject: Re: [gmx-users] (no subject)
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> I used the same .tpr file. I added  -dlb yes and  -
> reprod yes during mdrun
> with rerun option. Still I am not geting why energy, temp, 
> pressure are
> changing since I have same topology file and .trr file.

As I said last time, a parallel rerun cannot reproduce a run unless they're both run under the same conditions. Changing the options for the rerun cannot achieve this, because the original run probably had dynamic load balancing.

Mark

> Is there any bug in rerun option?
> Nilesh
> 
> On Mon, October 25, 2010 8:50 pm, Mark Abraham wrote:
> >
> 
> >
> > ----- Original Message -----
> > From: Nilesh Dhumal <ndhumal at andrew.cmu.edu>
> > Date: Tuesday, October 26, 2010 10:50
> > Subject: Re: [gmx-users] (no subject)
> > To: Discussion list for GROMACS users <gmx-users at 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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> >>
> >>
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