On 7/29/13 10:51 PM, S. Alireza Bagherzadeh wrote:
Hi All,
I am simulating a system in which I have two solid surfaces and I keep them
frozen during simulations. I also exclude the interactions between its
atoms to avoid spurious contribution to the virial pressure due to large
forces between them as suggested in the manual.
I run a nvt for equilibration and then I do the production run in an nve
ensemble; however, I am not getting good energy conservation. There is a
huge energy drift...
When I remove the solid surfaces, I will only have water molecules and
united atom methane molecules in my system. Using the same protocol I
obtain a very good energy conservation...
What happens if you unfreeze the frozen surfaces and run the same system?
Any insight on what might be wrong in my system would be very appreciated.
The contents of the .edr file will probably be informative, as you can identify
which energy term(s) is(are) most affected. It's all probably related to the
frozen surfaces themselves acting as an energy sink or something.
-Justin
Here is the mdp file:
;
; File 'mdout_nve.mdp' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Sun Jul 28 18:13:02 2013
;
; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/roe
include =
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.001
nsteps = 1000000
; For exact run continuation or redoing part of a run
init_step = 0
; Part index is updated automatically on checkpointing (keeps files
separate)
simulation_part = 1
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 100
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 10
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
; Step size (ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05
; 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 = 500
nstcalcenergy = -1
nstenergy = 500
; Output frequency and precision for .xtc file
nstxtcout = 0
xtc-precision = 1000
; This selects the subset of atoms for the .xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc_grps = HYDW HYDG SOL GAS SiO2 SiOH
; Selection of energy groups
energygrps = HYDW HYDG SOL GAS SiO2 SiOH
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 10
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic_molecules = no
; nblist cut-off
rlist = 1.7
; long-range cut-off for switched potentials
rlistlong = -1
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME-Switch
rcoulomb_switch = 1.3
rcoulomb = 1.5
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 1
epsilon_rf = 1
; Method for doing Van der Waals
vdw-type = shift
; cut-off lengths
rvdw-switch = 1.3
rvdw = 1.5
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Seperate tables between energy group pairs
energygrp_table =
; 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-06
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = No
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 1
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent = 80
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension = -1
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = no
nsttcouple = -1
nh-chain-length = 1
; Groups to couple separately
tc_grps = system
; Time constant (ps) and reference temperature (K)
tau_t = 0.2
ref_t = 370
; Pressure coupling
Pcoupl = no
Pcoupltype = Isotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 0.5
compressibility = 4.5e-05
ref_p = 40.0
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = No
; Random seed for Andersen thermostat
andersen_seed = 815131
; OPTIONS FOR QMMM calculations
QMMM = no
; Groups treated Quantum Mechanically
QMMM-grps =
; QM method
QMmethod =
; QMMM scheme
QMMMscheme = normal
; QM basisset
QMbasis =
; QM charge
QMcharge =
; QM multiplicity
QMmult =
; Surface Hopping
SH =
; CAS space options
CASorbitals =
CASelectrons =
SAon =
SAoff =
SAsteps =
; Scale factor for MM charges
MMChargeScaleFactor = 1
; Optimization of QM subsystem
bOPT =
bTS =
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing =
; Number of time points to use for specifying annealing in each group
annealing_npoints =
; List of times at the annealing points for each group
annealing_time =
; Temp. at each annealing point, for each group.
annealing_temp =
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
gen_temp = 370
gen_seed = -1
; OPTIONS FOR BONDS
constraints = none
; Type of constraint algorithm
constraint-algorithm = shake
; Do not constrain the start configuration
continuation = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 1e-10
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; 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
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl = SiOH SiOH SiO2 SiO2 SiOH SiO2
; WALLS
; Number of walls, type, atom types, densities and box-z scale factor for
Ewald
nwall = 0
wall_type = 9-3
wall_r_linpot = -1
wall_atomtype =
wall_density =
wall_ewald_zfac = 3
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = no
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file
nstdisreout = 100
; Orientation restraints: No or Yes
orire = no
; Orientation restraints force constant and tau for time averaging
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) and S to energy file
nstorireout = 100
; Dihedral angle restraints: No or Yes
dihre = no
dihre-fc = 1000
; Free energy control stuff
free-energy = no
init-lambda = 0
delta-lambda = 0
foreign_lambda =
sc-alpha = 0
sc-power = 0
sc-sigma = 0.3
nstdhdl = 10
separate-dhdl-file = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing = 0.1
couple-moltype =
couple-lambda0 = vdw-q
couple-lambda1 = vdw-q
couple-intramol = no
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps = SiO2 SiOH
freezedim = Y Y Y Y Y Y
cos-acceleration = 0
deform =
; Electric fields
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
; User defined thingies
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
--
==================================================
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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