[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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>
>
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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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