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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--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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