[gmx-users] Re: Questions
lloyd riggs
lloyd.riggs at gmx.ch
Tue Apr 17 16:10:15 CEST 2012
> I dont know. All I know is if I have it print one of the other deminsions, I get the other curves mentioned.
>
"When accusing the code of doing something wrong, "I don't know" isn't a very
good justification ;) The contents of pullx.xvg are the COM coordinates of the
reference group on the axis or axes along which the restraint was applied,
followed by the distance between the reference and pulled group, again along
each axis. In your case you should have the y-coordinate of the COM of the
reference, and dY, which represents the distance between the two groups along
the y-axis only. These values should be easy to confirm with g_traj and g_dist."
In my experience its rarely the code unless your writting something. That isnt what it was doing. It was printing the initial coordinates (COM) for the reference and pull group, and then the coordinates as they change, but not total difference.
>>> gromacs tools. Still when I use these the end results (energy
>> calculated at
>>> time 0 and end) are correct, but there is just a jump half way through
> >>>
> >>> Fatal error: Found 1 pull groups in traj_14.tpr, but 2 data columns in
> >>> pullf_14.xvg (expected 1)
> >>>
> >>> Maybe you confused options -ix and -if ?
> >>>
> >> Is this a possibility? Are your files named correctly with respect to
> >> their
> >> contents?
Maticulously named. Also, I always generate most of the files that can be output for namesake, and to keep track, as they usually (most) print the command line and date that they were generated via.
> >>
> >> Further, a complete .mdp file (or at least the complete pull code
> section)
> >> would
> >> be useful.
Included below (although Im terrified youll invalidate massive parallel work with a single comment) is the .mdp file I used for 10 of the runs, basically it was the only way I could get it to run. The time step is small because of the small molecule involved, however I painstakingly looked up all parameters ten times. Basically its only violation was with links, which seems to think S-O---H isnt supposed to roatate so much, but the molecules degrees of freedom (1/2 can rotate 360 from the other along a central axis) etc...
> >> -Justin
> >>
> >>> For more information and tips for troubleshooting, please check the
> >> GROMACS
> >>> website at http://www.gromacs.org/Documentation/Errors
> >>> -------------------------------------------------------
> >>>
>
I ma sure in 2 days I post that it was just like you said, a hidden return character or something...But I looked all day trying to find such. I will von morgen attempt to just cut and past in several text editors to see if that makes a difference. Thanks,
Stephan L. Watkins
_____________-generic MDP file--
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.1
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 1
epsilon_rf = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 1.2
; 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 = 0.16
; 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-5
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 = Nose-Hoover
nsttcouple = -1
nh-chain-length = 10
; Groups to couple separately
tc_grps = Protein Non-Protein
; Time constant (ps) and reference temperature (K)
tau_t = 2.0 2.0
ref_t = 300 300
; Pressure coupling
Pcoupl = Parrinello-Rahman
pcoupltype = isotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = all
; 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 = yes
gen_temp = 300
gen_seed = -1
; OPTIONS FOR BONDS
constraints = all-bonds
; Type of constraint algorithm
constraint_algorithm = lincs
; Do not constrain the start configuration
continuation = yes
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 0.0001
; 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 = 90
; 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 =
; 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 = umbrella
; Pull geometry: distance, direction, cylinder or position
pull_geometry = distance
; Select components for the pull vector. default: Y Y Y
pull_dim = N Y N
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1 = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0 = 1.5
pull_constr_tol = 1e-06
pull_start = yes
pull_nstxout = 10000
pull_nstfout = 10000
; Number of pull groups
pull_ngroups = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)
pull_group0 = A
pull_weights0 =
pull_pbcatom0 = 0
pull_group1 = B
pull_weights1 =
pull_pbcatom1 = 0
pull_vec1 = 0
pull_init1 = 0
pull_rate1 = 0.0005
pull_k1 = 2000
pull_kB1 = 2500
; 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 = yes
init_lambda = 0
delta_lambda = 5.0e-8
foreign_lambda = 0.05
sc-alpha = 0
sc_power = 1
sc_sigma = 0.2
nstdhdl = 10000
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 =
freezedim =
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
--
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