[gmx-users] Why is triclinic geometry not retained in confout.gro?
Jennifer Williams
Jennifer.Williams at ed.ac.uk
Tue Jul 7 19:18:06 CEST 2009
Hello gmx-users
I?m having problems with my mdrun (probably a newbie question). I?m
using the latest version of gromacs.
I have my .pdb file (or .gro), mdp and .top files ready and can
generate the .tpr file. When I run this (with an simple energy
minimisation) the simulation runs to completion (I?ve only tried a
very short run) but I get a strange confout.gro file as output. My
unit cell is triclinic and my input files (both .pdb or .gro) looks
fine in VMD.
The confgro.out file is strange in that the box has been converted to
cubic when I view it in VMD. Is this normal? Why doesn?t it retain the
triclinic shape I defined in the pdb file?
I?ve been over the topology but my inexperienced eyes can?t see
anything wrong. One thing I did notice is that when I looked at the
tpr file, all of my atom numbers were shifted by 1 with regards to my
topology file i.e
In the tpr file, the first angle listed is for atoms 364, 0 and 413
Angle:
nr: 9492
iatoms:
0 type=11 (ANGLES) 364 0 413
But in the topology file the first angle I have listed is for 365, 1 and 414.
[ angles ]
; ai aj ak funct c0 c1
365 1 414 1 109.04 289.095916
In my pdb and top file my atoms are labelled from 1-1071 whereas in
the .tpr file they are labelled from 0-1070. Is this something I
should be worried about?
Below I have pasted sections of my top file, my pdb file and my .mdp
file. I?d appreciate if someone could look over and see that my
triclinic unit cell is correctly defined (although the input file
looks OK when viewed in VMD).
If anyone has the time or inclination to try and run my files (if that
helps spot the error), I would be happy to e-mail them and would be
very grateful,
If you see anything else that looks odd, please feel free to point it
out as I am new to gromacs,
Thanks in advance,
Jenny
pdb
CRYST1 46.421 43.630 18.960 90.00 90.00 120.00 P 1 1
ATOM 1 SI X 1 -22.104 -1.646 -1.173 1.00 0.00 SI
ATOM 2 SI X 1 8.325 -18.877 8.329 1.00 0.00 SI
ATOM 3 SI X 1 27.146 -12.854 3.831 1.00 0.00 SI
ATOM 4 SI X 1 -14.415 -11.322 4.375 1.00 0.00 SI
ATOM 5 SI X 1 -10.624 -15.731 -7.960 1.00 0.00 SI
...
ATOM 289 O X 1 19.588 -18.099 7.519 1.00 0.00
ATOM 290 O X 1 -19.450 0.838 -2.667 1.00 0.00
...
ATOM 794 O X 1 22.966 -15.478 -8.908 1.00 0.00
ATOM 795 O X 1 17.234 -5.878 -2.785 1.00 0.00
ATOM 796 OH X 1 -7.634 -18.464 -3.746 1.00 0.00
ATOM 797 H X 1 -7.655 -18.213 -4.662 1.00 0.00 H
ATOM 798 OH X 1 7.669 -17.509 7.819 1.00 0.00
ATOM 799 H X 1 8.061 -17.122 7.046 1.00 0.00 H
....
ATOM 1068 OH X 1 4.808 -14.731 1.210 1.00 0.00
ATOM 1069 H X 1 3.887 -14.515 1.123 1.00 0.00 H
ATOM 1070 OH X 1 18.839 0.763 -8.266 1.00 0.00
ATOM 1071 H X 1 18.283 0.835 -9.032 1.00 0.00 H
END
Topology file
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 no 1.0 1.0
;
;
[ atomtypes ]
; type mass charge ptype c6 c12
SI 28.08 1.28 A 0.000 0.00
O 15.999 -0.64 A 0.2708 1.538176
OH 15.999 -0.53 A 0.30 1.538176
H 1.008 0.21 A 0.000 0.000
;
[ moleculetype ]
; Name nrexcl
MCM 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 SI 1 MCM SI 1 1.2804993 28.086
2 SI 1 MCM SI 2 1.2804993 28.086
3 SI 1 MCM SI 3 1.2804993 28.086
4 SI 1 MCM SI 4 1.2804993 28.086
5 SI 1 MCM SI 5 1.2804993 28.086
...
289 O 1 MCM O 289 -0.64024965 15.9994
290 O 1 MCM O 290 -0.64024965 15.9994
...
794 O 1 MCM O 794 -0.64024965 15.9994
795 O 1 MCM O 795 -0.64024965 15.9994
796 OH 1 MCM OH 796 -0.52612471 15.9994
797 H 1 MCM H 797 0.20599988 1.00797
798 OH 1 MCM OH 798 -0.52612471 15.9994
799 H 1 MCM H 799 0.20599988 1.00797
...
1068 OH 1 MCM OH 1068 -0.52612471 15.9994
1069 H 1 MCM H 1069 0.20599988 1.00797
1070 OH 1 MCM OH 1070 -0.52612471 15.9994
1071 H 1 MCM H 1071 0.20599988 1.00797
[ bonds ]
; ai aj funct c0 c1 c2 c3
796 797 1 0.0945 313800
798 799 1 0.0945 313800
...
286 289 1 0.16 251040
8 1058 1 0.16 251040
[ angles ]
; ai aj ak funct c0 c1
365 1 414 1 109.04 289.095916
365 1 631 1 109.04 289.095916
123 1066 1067 1 109.04 289.095916
194 1068 1069 1 109.04 289.095916
51 1070 1071 1 109.04 289.095916
[ dihedrals ]
; ai aj ak al funct c0 c1
486 286 289 225 5 0.0000 0.0000 0.0000 0.0000
1016 286 289 225 5 0.0000 0.0000 0.0000 0.0000
510 237 773 68 5 0.0000 0.0000 0.0000 0.0000
785 237 773 68 5 0.0000 0.0000 0.0000 0.0000
[ system ]
; Name
MCM
[ molecules ]
; Compound #mols
MCM 1
;
Mdp file
; File 'mdout.mdp' was generated
; By user: jwillia4 (353773)
; On host: vlxhead2
; At date: Fri Jun 26 15:47:37 2009
;
; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include = -I../top
; e.g.: -DI_Want_Cookies -DMe_Too
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.0001
nsteps = 500
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files separate)
simulation_part = 1
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
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol =
emstep =
; Max number of iterations in relax_shells
niter =
; Step size (ps^2) for minimization of flexible constraints
fcstep =
; Frequency of steepest descents steps when doing CG
nstcgsteep =
nbfgscorr =
; TEST PARTICLE INSERTION OPTIONS
rtpi =
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 10
nstvout = 10
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 = 10
; 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 =
; ns algorithm (simple or grid)
ns_type =
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic_molecules = yes
; nblist cut-off
rlist = 0.9
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Ewald
rcoulomb-switch = 0
rcoulomb = 0.9
; Relative dielectric constant for the medium and the reaction field
epsilon_r =
epsilon_rf =
; 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 = No
; Extension of the potential lookup tables beyond the cut-off
table-extension =
; 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 =
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = No
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm =
; Frequency of calculating the Born radii inside rlist
nstgbradii =
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii =
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent =
; Salt concentration in M for Generalized Born models
gb_saltconc =
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha =
gb_obc_beta =
gb_obc_gamma =
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
sa_surface_tension =
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = nose-hoover
; Groups to couple separately
tc-grps = MCM
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 300
; Pressure coupling
Pcoupl = No
Pcoupltype =
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p =
compressibility =
ref-p =
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = no
; Random seed for Andersen thermostat
andersen_seed =
; OPTIONS FOR QMMM calculations
QMMM = no
; Groups treated Quantum Mechanically
QMMM-grps =
; QM method
QMmethod =
; QMMM scheme
QMMMscheme =
; 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 =
; Optimization of QM subsystem
bOPT =
bTS =
; 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 = 300
gen_seed = 173529
; OPTIONS FOR BONDS
constraints = none
; Type of constraint algorithm
constraint-algorithm = Lincs
; 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 = 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 = 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 =
; 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
sc-alpha = 0
sc-power = 0
sc-sigma = 0.3
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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