[gmx-users] attachs ; question tree messages:how?

Mon Nov 3 16:30:01 CET 2003

Dear Users,  Nuno

Sorry,  I attached here my three files and seek your help to find the problem, because the Gromacs stopped when a make mdrun.

; .gro file---------

Argon

100

1Argon AR 1 1.024 0.778 0.841

2Argon AR 2 0.067 1.713 0.853

3Argon AR 3 1.246 0.981 0.266

4Argon AR 4 0.204 0.357 0.233

5Argon AR 5 2.079 0.289 1.658

6Argon AR 6 0.962 0.295 1.403

7Argon AR 7 1.354 0.007 1.372

8Argon AR 8 1.632 1.046 0.936

9Argon AR 9 1.847 1.282 0.369

10Argon AR 10 1.930 0.924 0.641

11Argon AR 11 0.832 1.824 0.279

12Argon AR 12 1.906 1.018 1.961

13Argon AR 13 0.409 1.827 1.733

14Argon AR 14 1.695 1.810 0.181

15Argon AR 15 0.945 0.299 0.758

16Argon AR 16 0.246 0.857 1.711

17Argon AR 17 0.782 1.460 0.014

18Argon AR 18 0.556 1.150 0.250

19Argon AR 19 1.249 1.188 0.730

20Argon AR 20 1.131 1.337 1.192

21Argon AR 21 0.975 0.575 0.432

22Argon AR 22 1.908 0.095 0.363

23Argon AR 23 0.365 0.869 1.185

24Argon AR 24 1.085 1.375 0.330

25Argon AR 25 2.038 1.699 0.416

26Argon AR 26 0.081 1.315 1.745

27Argon AR 27 1.456 0.077 0.229

28Argon AR 28 0.248 0.950 0.488

29Argon AR 29 0.864 0.844 0.092

30Argon AR 30 1.383 0.182 0.675

31Argon AR 31 0.531 0.244 1.647

32Argon AR 32 1.438 1.809 0.610

33Argon AR 33 1.268 0.843 1.901

34Argon AR 34 0.578 0.153 0.363

35Argon AR 35 1.047 1.229 1.862

36Argon AR 36 0.489 1.196 1.907

37Argon AR 37 0.152 0.522 0.642

38Argon AR 38 1.874 1.381 0.881

39Argon AR 39 1.657 0.904 0.211

40Argon AR 40 1.163 2.064 1.971

41Argon AR 41 0.546 1.176 0.756

42Argon AR 42 0.131 1.097 0.903

43Argon AR 43 0.340 0.364 1.195

44Argon AR 44 0.669 2.085 2.050

45Argon AR 45 2.053 0.681 0.996

46Argon AR 46 2.079 1.664 2.032

47Argon AR 47 0.393 1.374 1.157

48Argon AR 48 1.326 0.832 1.196

49Argon AR 49 0.240 0.893 0.049

50Argon AR 50 1.040 0.101 0.359

51Argon AR 51 0.845 0.375 0.063

52Argon AR 52 0.752 2.003 0.694

53Argon AR 53 2.033 0.693 0.287

54Argon AR 54 1.137 2.010 0.976

55Argon AR 55 0.541 0.633 0.350

56Argon AR 56 2.070 0.218 0.976

57Argon AR 57 0.646 1.791 1.358

58Argon AR 58 1.793 0.084 1.971

59Argon AR 59 0.761 0.545 1.095

60Argon AR 60 0.173 0.056 0.616

61Argon AR 61 1.429 0.653 0.765

62Argon AR 62 0.706 1.490 0.527

63Argon AR 63 0.563 0.629 1.478

64Argon AR 64 0.204 1.387 0.571

65Argon AR 65 0.728 0.074 1.121

66Argon AR 66 0.870 1.007 0.512

67Argon AR 67 1.901 1.857 1.186

68Argon AR 68 2.091 0.564 1.980

69Argon AR 69 0.620 1.667 0.938

70Argon AR 70 0.611 1.171 1.486

71Argon AR 71 1.766 0.863 1.361

72Argon AR 72 1.660 0.616 1.823

73Argon AR 73 0.993 0.478 1.774

74Argon AR 74 1.784 2.040 0.765

75Argon AR 75 0.395 1.791 0.510

76Argon AR 76 1.263 1.733 0.164

77Argon AR 77 0.044 0.628 1.411

78Argon AR 78 0.866 2.041 1.649

79Argon AR 79 1.228 0.392 1.086

80Argon AR 80 1.392 0.556 0.353

81Argon AR 81 0.505 0.301 0.782

82Argon AR 82 0.973 0.814 1.430

83Argon AR 83 0.215 2.089 1.417

84Argon AR 84 1.801 0.442 0.631

85Argon AR 85 0.165 2.011 0.196

86Argon AR 86 2.015 1.919 1.688

87Argon AR 87 0.529 0.743 0.782

88Argon AR 88 1.064 1.619 0.761

89Argon AR 89 0.787 1.054 1.092

90Argon AR 90 1.313 0.397 2.048

91Argon AR 91 1.817 0.157 1.361

92Argon AR 92 0.019 1.173 1.332

93Argon AR 93 1.663 0.436 1.074

94Argon AR 94 0.474 0.549 1.992

95Argon AR 95 0.333 2.018 1.008

96Argon AR 96 0.742 0.864 1.809

97Argon AR 97 0.245 0.130 1.950

98Argon AR 98 0.428 1.701 0.055

99Argon AR 99 1.736 0.426 0.139

100Argon AR 100 0.149 1.315 0.130

5.10000 5.10000 5.10000

; ------- .top file

; Argon

[ defaults ]

; nb-function combinationrule

1 2

[ atomtypes ]

; type mass charge ptype sig eps

AR 1.0 0.0 A 1.0 1.0 

[ moleculetype ]

; molname nrexcl

Argon 1

[ atoms ]

; id at type res nr residu name at name cg nr

1 AR 1 Argon AR 1 

[ system ]

; systemname

Argon

[ molecules ]

; molecule number

Argon 100

;-----mdp file  

; VARIOUS PREPROCESSING OPTIONS

;title = Yo

;cpp = /lib/cpp

title = Albert-md

cpp = c:\Progra~1\Gromacs\bin\cpp.exe

include = 

define = 

;

; RUN CONTROL PARAMETERS

integrator = md

; start time and timestep in ps

tinit = 0.0

dt = 0.002

nsteps = 1000

; after checkpoint or tpbconv restart we can start on step > 0

;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

; Temperature, friction coefficient (amu/ps) and random seed

bd-temp = 300

bd-fric = 0

ld_seed = 1993

;

; ENERGY MINIMIZATION OPTIONS

; Force tolerance and initial step-size

emtol = 0.001

emstep = 0.1

; Max number of iterations in relax_shells

niter = 100

; Step size (1/ps^2) for minimization of flexible constraints

fcstep = 0

; Frequency of steepest descents steps when doing CG

nstcgsteep = 1000

;

; OUTPUT CONTROL OPTIONS

; Output frequency for coords (x), velocities (v) and forces (f)

nstxout = 10

nstvout = 10

nstfout = 0

; Checkpointing helps you continue after crashes

;nstcheckpoint = 1000 ;????

; Output frequency for energies to log file and energy file

nstlog = 0

nstenergy = 1

; Output frequency and precision for xtc file

nstxtcout = 0

xtc_precision = 1000

; 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 = Argon

;

; NEIGHBORSEARCHING PARAMETERS

; nblist update frequency

nstlist = 1

; ns algorithm (simple or grid)

ns_type = simple

; Periodic boundary conditions: xyz or no

pbc = xyz

; nblist cut-off 

rlist = 2.5

;domain-decomposition = no ;???????

;

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype = Cut-off

rcoulomb_switch = 0 ;???? original -

rcoulomb = 2.5

; Dielectric constant (DC) for cut-off or DC of reaction field

epsilon_r = 1

; Method for doing Van der Waals

vdw-type = Cut-off

; cut-off lengths 

rvdw_switch = 0 ; ????? original -

rvdw = 2.5

; Apply long range dispersion corrections for Energy and Pressure

DispCorr = No

; Spacing for the PME/PPPM FFT grid

fourierspacing = 0.12

; FFT grid size, when a value is 0 fourierspacing will be used

fourier_nx = 10

fourier_ny = 10

fourier_nz = 10

; EWALD/PME/PPPM parameters

pme_order = 4

ewald_rtol = 1e-05

ewald_geometry = 3d

surface_epsilon = 0 ;?????? original: epsilon_surface 

optimize_fft = no

;

; GENERALIZED BORN ELECTROSTATICS

; Algorithm for calculating Born radii

;gb_algorithm = Still ;????

; Frequency of calculating the Born radii inside rlist

;nstgbradii = 1 ;????

; Cutoff for Born radii calculation; the contribution from atoms

; between rlist and rgbradii is updated every nstlist steps

;rgbradii = 2 ;????

; Salt concentration in M for Generalized Born models

;gb_saltconc = 0 ;??????

;

; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)

;implicit_solvent = No ;???????

;

; OPTIONS FOR WEAK COUPLING ALGORITHMS

; Temperature coupling 

tcoupl = no

; Groups to couple separately

tc-grps = Argon

; Time constant (ps) and reference temperature (K)

tau_t = 0.1

ref_t = 120

; Pressure coupling 

Pcoupl = no

Pcoupltype = Isotropic

; Time constant (ps), compressibility (1/bar) and reference P (bar)

tau_p = 1.0

compressibility = 

ref_p = 1.0

; Random seed for Andersen thermostat

;andersen_seed = 815131 ;?????

;

; 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 = no

gen_temp = 120

gen_seed = 173529

; OPTIONS FOR BONDS 

constraints = none

; Type of constraint algorithm

constraint_algorithm = Lincs

; Do not constrain the start configuration

unconstrained_start = 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 = 

; 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 = Equal

; Use sqrt of the time averaged times the instantaneous violation

disre_mixed = no

disre_fc = 1000

disre_tau = 1.25

; 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) to energy file

nstorireout = 100

; Dihedral angle restraints: No, Simple or Ensemble

;dihre = No ;??????

;dihre-fc = 1000 ;?????

;dihre-tau = 0

; Output frequency for dihedral values to energy file

;nstdihreout = 100 ;????? 

; Free energy control stuff

free_energy = no

init_lambda = 0

delta_lambda = 0

sc-alpha = 0

sc-sigma = 0.3

; Non-equilibrium MD stuff

acc-grps = 

accelerate = 

freezegrps = 

freezedim = 

cos-acceleration = 0

; 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

Many Thanks

Albert

"Nuno R. L. Ferreira" <nunolf at ci.uc.pt> wrote:
I'm so sorry gmx's, but sometimes I can't see the attachs.(tranfer encoded
by smth)
Why don't you send it as plain text?

BTW, a silly question. When I reply to someone, I was never able to put my
answer just below the question tree in the gmx mail-list. Usually I do a
reply to the gmx-digest e-mail, discarting all the messages except the one
to reply for. Then, just change the subject to the question posed.

At#12539;
Nuno

#######################################
Nuno Ricardo Santos Loureiro da Silva Ferreira
Departamento de Qu#21255;ica
Faculdade de Ci#40617;cias e Tecnologia
Universidade de Coimbra
3004-535 Coimbra - Portugal
Fax: +351 239 827703 - www.biolchem.qui.uc.pt
#######################################

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