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.willi...@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 > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
