Shuangxing Dai wrote:
Thanks for the response.
Yes, I know that large fluctuations will be expected. But why the
average was not even correct? Also, how can I reach some state ( some
pressre and temperature) and know/tell that the system is
in equilibrium if the average is not correct with large fluctuation? I
mean I do not know the criteria of Gromacs. Or maybe my procedure is wrong?
You've only run 100 ps total equilibration. For an extremely high temperature,
I might expect it to take quite a bit longer, especially since you're dealing
with a system that will be subject to large fluctuations (due to its size).
-Justin
Message: 1
Date: Mon, 05 Jul 2010 10:39:30 -0400
From: "Justin A. Lemkul" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] pressure coupling
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4c31eea2.7070...@vt.edu <mailto:4c31eea2.7070...@vt.edu>>
Content-Type: text/plain; charset=UTF-8; format=flowed
Shuangxing Dai wrote:
Hi, all,
I am trying to do anisotropic coupling using Parrinello-Rahman. I
want to reach the equilibrium state at 1000K, 0.1MPa( 1 bar). However,
I find that the fluctuation is so large ( p=80.22 bar, T=1007.23 K,
fluctuation is 626 bar for pressure and 11.21 K for temperature.) I run
energy minimization first, then Berenderson pressure coupling for 50 ps,
finally Parrinello-Rahman pressure coupling for 50 ps. Anyone has
experience on anisotropic coupling and know why?
My system has just 4000 atoms. This is my .mdp file:
For a small system, large fluctations in the pressure are to be expected:
http://www.gromacs.org/Documentation/Terminology/Pressure
-Justin
;define = -DPOSRES
; RUN CONTROL PARAMETERS =
integrator = sd
; start time and timestep in ps =
tinit = 0
dt = 0.001
nsteps = 50000
; number of steps for center of mass motion removal =
nstcomm = 100
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 0
nstvout = 0
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 10
nstenergy = 10
; Output frequency and precision for xtc file =
nstxtcout = 10
xtc-precision = 1000
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 20
; ns algorithm (simple or grid) =
ns_type = grid
;OPTIONS FOR PRESSURE COUPLING
Pcoupl = Parrinello-Rahman
pcoupltype = anisotropic
tau_p = 5
compressibility = 2.1645e-07 2.1645e-07 2.7322e-07 0 0 0
ref_p = 1 1 1 0 0 0
;OPTIONS FOR TEMPERATURE COUPLING
tc_grps = system
tau_t = 1
ref_t = 1000
; OPTIONS FOR BONDS =
constraints = hbonds
; Type of constraint algorithm =
constraint-algorithm = Lincs
; Do not constrain the start configuration =
unconstrained-start = no
; Relative tolerance of shake =
shake-tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order = 12
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle = 30
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic_molecules = no
; nblist cut-off
rlist = 1
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 6
ewald_rtol = 1e-4
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
I used the same procedure to reach different state ( like 0.01 K, 100K,
300K, 500K, 800K, 1000K). Only the 0.01 K got the correct average
pressure and small fluctuation.
T p(bar) delta p T (K) delta T
0.01 1.03E+00 2.12E+00 9.95E-03 1.21E-04
100 5.48359 71.5565 91.198 1.25218
300 2.62807 162.926 290.324 3.36594
500 16.6356 1048.76 492.616 5.45231
800 59.3245 594.773 799.314 9.18876
1000 80.2257 626.789 1007.23 11.2159
Thanks in advance,
Shuangxing Dai
Thanks,
Shuangxing Dai
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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