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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