[gmx-users] SUSPICIOUS: Pressure scaling ...
Tandia, Adama
TandiaA at Corning.com
Mon Jul 26 22:00:16 CEST 2004
Dear ALL:
I'm running (or trying to run) a MD with the following .mdp file ( s system composed of 10 different ions)
A room temperature and 1 bar:
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; VARIOUS PREPROCESSING OPTIONS =
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
title = My Structure
cpp = /lib/cpp
include =
define =
; RUN CONTROL PARAMETERS =
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
integrator = md
; start time and timestep in ps =
tinit = 0.0
dt = 0.002
nsteps = 60000
; number of steps for center of mass motion removal =
nstcomm = 1
; OUTPUT CONTROL OPTIONS =
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for xtc file =
nstxtcout = 5000
xtc_precision = 5000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps = Si O Al B Mg Ca Ba Sr As Na
; Selection of energy groups =
energygrps = Si O Al B Mg Ca Ba Sr As Na
; NEIGHBORSEARCHING PARAMETERS =
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
;rlist = 1.5
rlist = 0.75
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; Method for doing electrostatics =
coulombtype = Cut-off
rcoulomb_switch = 0.0
;rcoulomb = 1.8
rcoulomb = 0.8
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 20
; Method for doing Van der Waals =
vdw_type = Cut-off
; cut-off lengths =
rvdw_switch = 0.9
;rvdw = 1.8
rvdw = 0.8
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx = 10
fourier_ny = 10
fourier_nz = 10
; EWALD/PME/PPPM parameters =
pme_order = 4
ewald_rtol = 1e-05
epsilon_surface = 0
optimize_fft = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = SiG O Al B Mg Ca Ba Sr As Na
; Time constant (ps) and reference temperature (K) =
tau_t = 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0
ref_t = 300.0 300.0 300.0 300.0 300.0 300.0 300.0 300.0 300.0 300.0
; Pressure coupling =
Pcoupl = Berendsen
Pcoupltype = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 25.0
;compressibility = 2.5E-7
compressibility = 9.804E-7
ref_p = 1.0
; SIMULATED ANNEALING CONTROL =
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
annealing = no no no no no no no no no no
; Time at which temperature should be zero (ps) =
;zero_temp_time = 0
; GENERATE VELOCITIES FOR STARTUP RUN =
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
gen_vel = yes
gen_temp = 300.0
gen_seed = 473529
; OPTIONS FOR BONDS =
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
constraints = none
; Type of constraint algorithm =
constraint_algorithm =
; 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 = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 30
; Convert harmonic bonds to morse potentials =
morse = no
; NMR refinement stuff =
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; Distance restraints type: No, Simple or Ensemble =
disre = No
; Force weighting of pairs in one distance restraint: Equal or Conservative =
disre_weighting = Equal
; Use sqrt of the time averaged times the instantaneous violation =
disre_mixed = no
disre_fc = 1000
disre_tau = 1.25
; Output frequency for pair distances to energy file =
nstdisreout = 100
; Free energy control stuff =
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
free_energy = no
init_lambda = 0
delta_lambda = 0
sc-alpha = 0
sc-sigma = 0.3
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
I searched the user list and I tried many different values of tau_p (from 0.1 to 70 (!) )but that did not help at all.
The same .mdp file adapted to Si only works perfectly!
Thanks in advance for the help.
Adama Tandia
Modeling & Simulation
Corning INC
Corning, NY 14831 USA
Tel: 607 248 1036
Fax: 607 974 3405
www.corning.com <www.corning.com>
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