[gmx-users] RE: average pressure of a system

[Dallas Warren]

Also remember that here you are dealing with the measurement of a macroscopic property on a microscopic scale.

As Justin has alluded to, the only manner in which you can make the variation / fluctuations in the pressure smaller is by increase the total number of particles in the system.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Dwey Kauffman
> Sent: Wednesday, 11 September 2013 12:57 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] RE: average pressure of a system
> 
> Hi Dallas and Justin,
> 
>   Thanks for the reply. Yes, I did plot pressure changes over time by
> g_energy and I have been aware of the note  at
> http://www.gromacs.org/Documentation/Terminology/Pressure
> 
> I am concerned about the average pressure is because our experiment
> shows
> that our target membrane protein is a hexamer and our observation is
> that
> variation of system pressure seems causing hexamer or dimer
> dissociation.
> Also, it is quite sensitive to pressure fluctuation. Such a fluctuation
> of
> pressure certainly brings my attention in this specific case, because
> life
> does not exist at large variations of system pressure.
> If not because of multimer dissociation likely caused by pressure
> fluctuation, I agree with both of you.
> 
> I also run longer simulations like 20 ns and 30 ns
> 
> ### 20 ns
> 
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -----------------------------------------------------------------------
> --------
> Pressure                   0.886396       0.84    162.655    1.38476
> (bar)
> 
> ## 30 ns
> 
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -----------------------------------------------------------------------
> --------
> Pressure                    1.69086       0.58    162.879    3.35668
> (bar)
> 
> 
> Running longer simulations seems to me that the improvement of system
> pressure is not helpful too much.
> If I need to modify mdp file, what it would be ?
> 
> 
> 
> Many thanks,
> 
> Dwey
> 
> 
> My mdp file for NPT  is used in the simulation like
> 
> define          = -DPOSRES
> 
> integrator      = md
> nsteps          = 500000
> dt                  = 0.002
> 
> nstxout         = 100
> nstvout         = 100
> nstenergy       = 100
> nstlog          = 100
> 
> continuation    = yes
> constraint_algorithm = lincs
> constraints     = all-bonds
> lincs_iter      = 1
> lincs_order     = 4
> 
> ns_type         = grid
> nstlist         = 5
> rlist           = 1.2
> rcoulomb        = 1.2
> rvdw            = 1.2
> 
> coulombtype     = PME
> pme_order       = 4
> fourierspacing  = 0.16
> 
> tcoupl          = Nose-Hoover
> tc-grps         = Protein DPPC  SOL_CL
> tau_t           = 0.5   0.5     0.5
> ref_t           = 323   323     323
> 
> pcoupl          = Parrinello-Rahman
> pcoupltype      = semiisotropic
> tau_p           = 5.0
> ref_p           = 1.0   1.0
> compressibility = 4.5e-5        4.5e-5
> 
> pbc                 = xyz
> 
> DispCorr        = EnerPres
> 
> gen_vel         = no
> 
> 
> nstcomm         = 1
> comm-mode       = Linear
> comm-grps       = Protein_DPPC SOL_CL
> 
> refcoord_scaling = com
> cutoff-scheme = Verlet
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/average-pressure-of-a-system-
> tp5011095p5011098.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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