[gmx-users] TPI Results differ in v4.5.7 and v4.6.1
Niels Müller
uni at nielsm.de
Mon Jun 24 11:19:06 CEST 2013
Hi GMX Users,
We are computing the chemical potential of different gas molecules in a polymer melt with the tpi integrator.
The computations are done for CO2 and CH4.
The previous computations were done with v4.5.5 or 4.5.7 and gave equal results.
I recently switched to gromacs version 4.6.1, and the chemical potential computed by this version is shifted by a nearly constant factor, which is different for the two gas molecules.
We are perplexed what causes this shift. Was there any change in the new version that affects the tpi integration? I will provide the mdp file we used below.
The tpi integration is run on basis of the last 10 ns of a 30 ns NVT simulation with 'mdrun -rerun'.
Best regards,
Niels.
#########################
The mdp file:
#########################
; VARIOUS PREPROCESSING OPTIONS
cpp = cpp
include =
define =
; RUN CONTROL PARAMETERS
integrator = tpi
; 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
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Temperature, friction coefficient (amu/ps) and random seed
bd-fric = 0.5
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 100
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
; Step size (1/ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 100
nstvout = 0
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 100
; Output frequency for energies to log file and energy file
nstlog = 100
nstenergy = 100
; 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 =
; Selection of energy groups
energygrps =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 0.9
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = pme
rcoulomb-switch = 0
rcoulomb = 0.9
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 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 = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = 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 = 2
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = V-rescale
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 318
; Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 5.0
compressibility = 4.5e-5
ref_p = 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing = no
; 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 = yes
gen_temp = 400
gen_seed = 1993
; OPTIONS FOR BONDS
;constraints = none
constraints = all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
unconstrained-start = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 1e-04
; 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 =
; 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) to energy file
nstorireout = 100
; Dihedral angle restraints: No, Simple or Ensemble
dihre = No
dihre-fc = 1000
dihre-tau = 0
; Output frequency for dihedral values to energy file
nstdihreout = 100
; Free energy control stuff
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-sigma = 0.3
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
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