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

[Justin Lemkul]

On 9/10/13 10:56 PM, Dwey Kauffman wrote:
> 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.

True, but thermostats allow temperatures to oscillate on the order of a few K, 
and that doesn't happen on the macroscopic level either.  Hence the small 
disconnect between a system that has thousands of atoms and one that has 
millions or trillions.  Pressure fluctuations decrease on the order of sqrt(N), 
so the system size itself is a determining factor for the pressure fluctuations. 
  As previous discussions have rightly concluded, pressure is a somewhat 
ill-defined quantity in molecular systems like these.

> 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.

And yet neither is statistically indistinguishable from the value of 1, given 
that the standard deviations are ~163 bar.

> If I need to modify mdp file, what it would be ?
>

You could try altering tau_p, but I doubt there is any value in doing so.

-Justin

>
>
> 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
>
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> --
> 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.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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