[gmx-users] Why is triclinic geometry not retained in confout.gro?
Tsjerk Wassenaar
tsjerkw at gmail.com
Tue Jul 7 23:06:19 CEST 2009
Hi Jenny,
Check chapter 3 of the manual regarding PBC. There is no box in PBC (a
box defines PBC, but PBC does not define a box). The rectangular brick
is just one of the ways to represent the unit cell. If you insist in
seeing a triclinic unit cell, use trjconv -ur triclinic -pbc inbox.
Cheers,
Tsjerk
On Tue, Jul 7, 2009 at 7:18 PM, Jennifer
Williams<Jennifer.Williams at ed.ac.uk> wrote:
>
> 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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> Scotland, with registration number SC005336.
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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