[gmx-users] Simple L-J Particles' simulation
Albert Sun
albert_sun9 at yahoo.com
Mon Oct 27 17:29:01 CET 2003
Dear Users,
A few weeks ago, I got files from Dr. David van der Spoel on a simple L-J problem " argon". They worked well.
Then I created a new .gro file (as attached) and used same top and mdp files from Dr. David.
However, when I started mdrun, it stopped there, I checked that the .trr had no output.
I minimised the system erergy one or two times respectively before run mdrun, it has same problem.
"Back Off! I just backed up ener.edr to ./#ener.edr.2#
Group 0 ( topatom) has 3 elements
Group 1 ( botatom) has 3 elements
Group 2 ( System) has 100 elements
Group 3 ( argon) has 94 elements
Select a group: 2
starting mdrun 'Argon'
5000 steps, 10.0 ps "
No reuslts come out
Would greatly appreciate if you could advise me what could cause this problem.
Thanks in advance
David <spoel at xray.bmc.uu.se> wrote:
On Wed, 2003-09-24 at 18:04, Albert Sun wrote:
> Dear Groeten, David and Gmx-users,
> I have a few stupid questions:
> How to simulate simple Lennard Jones particles in Gromacs?
> In .top file, we don't need input bond and angle data, is it right?
> How to specify force field in .top file
here's an example from the gmx testset.
>
> Greatly appreciate your clarification.
>
> Thanks
>
> Albert
> Albert Sun wrote:
> Dear David and Gmx-users,
> I have a few stupid questions:
> How to simulate simple Lennard Jones particles in Gromacs?
> In .top file, we don't need input bond and angle data, is it
> right?
> How to specify force field in .top file?
>
> Greatly appreciate your clarification.
>
> Thanks
>
> Albert
> Albert Sun wrote:
> Dear Groeten, David
> How to start simple Lennard Jones particles in
> Gromacs?
> by specify force field: ffgmx
> thanks!
>
> Albert
>
> David wrote:
> On Sat, 2003-09-20 at 21:09, Albert Sun wrote:
> > Hi, Dear Anton,
> > Atoms exploded problem still remains, when I
> view .trr file by VMD,
> > all atoms suddenly disappear.
> > I tried ngmx, it had error: float exception.
> > I tried trjconv -dump, it showed warning:
> "no output, trajectory ended
> > at 3"
> >
> > could you give me more hints ?
>
>
> It seems to me that you have just a weird
> system with all atoms placed
> in a plane, and large forces between them.
>
> If you intend to simulate some sort of two
> dimensional crystal, you
> should probably start with simple Lennard
> Jones particles.
> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, Dept. of Cell and
> Molecular Biology
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax : 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org
> http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> _______________________________________________
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Argon
125
1Argon AR 1 4.895 1.092 4.682 -1.1326 1.5028 -0.3139
2Argon AR 2 1.156 0.524 1.448 1.2795 -0.2792 0.8730
3Argon AR 3 0.985 2.029 2.012 1.7219 -0.7373 -1.1915
4Argon AR 4 4.924 0.489 3.687 -0.5243 2.0315 -0.3342
5Argon AR 5 0.464 1.205 3.037 -0.6154 0.8562 -0.4888
6Argon AR 6 1.330 2.145 0.086 -0.4231 -0.7396 0.5885
7Argon AR 7 0.460 1.527 1.252 0.2134 0.1881 -0.0428
8Argon AR 8 0.591 4.622 2.154 -0.1886 0.5678 0.9706
9Argon AR 9 1.235 0.835 3.569 -0.0540 0.7621 0.2812
10Argon AR 10 4.860 2.987 4.888 0.7087 0.8855 -0.0666
11Argon AR 11 1.808 3.150 0.377 1.0813 -0.0937 -0.2159
12Argon AR 12 0.943 2.452 0.967 -1.2118 0.9035 0.1153
13Argon AR 13 0.544 3.039 2.228 -0.4095 1.2861 -0.7635
14Argon AR 14 5.040 1.969 2.361 -2.3891 -0.7822 -0.2271
15Argon AR 15 3.960 4.501 0.337 -0.9374 -0.6907 1.0124
16Argon AR 16 1.172 3.746 0.959 0.1516 -0.1523 0.4900
17Argon AR 17 2.280 3.868 1.392 0.1532 0.2206 0.4628
18Argon AR 18 1.233 3.746 2.096 1.6713 0.7138 1.8370
19Argon AR 19 5.024 2.452 3.417 0.2566 -0.2714 -0.0202
20Argon AR 20 0.175 3.430 3.782 -0.1056 1.4345 0.2331
21Argon AR 21 2.726 1.305 0.712 -0.0390 -1.5948 -0.5293
22Argon AR 22 0.207 3.874 1.631 -2.4302 -0.0397 1.9954
23Argon AR 23 0.285 4.788 3.105 0.2782 0.9295 0.2530
24Argon AR 24 1.176 2.816 4.145 -0.1406 0.4559 -1.2429
25Argon AR 25 4.318 4.740 4.495 0.5516 0.4663 2.1848
26Argon AR 26 1.864 4.798 4.629 1.5901 -1.5084 0.3228
27Argon AR 27 0.344 0.831 0.485 -0.3221 1.4094 1.0212
28Argon AR 28 2.268 0.316 3.079 -0.7959 1.1356 1.9309
29Argon AR 29 2.107 4.413 2.785 -0.7391 -0.3921 0.0283
30Argon AR 30 0.965 0.165 4.325 0.0312 0.3614 0.0970
31Argon AR 31 2.238 1.695 4.984 0.2919 -0.8347 -0.7021
32Argon AR 32 1.341 1.176 0.676 0.8544 0.2996 -0.6172
33Argon AR 33 0.908 2.289 3.208 0.5111 0.0979 1.3060
34Argon AR 34 1.847 0.781 4.379 1.4208 0.4866 0.5295
35Argon AR 35 0.366 2.406 4.456 -0.1472 0.4125 1.2066
36Argon AR 36 2.901 2.956 1.493 1.2892 -0.6305 1.0128
37Argon AR 37 5.058 2.524 1.464 0.0022 -1.7319 -0.4964
38Argon AR 38 2.803 2.480 3.679 -0.0907 1.2107 -1.8332
39Argon AR 39 1.886 2.325 3.241 0.6276 -1.8375 -0.8451
40Argon AR 40 0.836 3.294 4.991 0.6273 0.7660 -1.3883
41Argon AR 41 2.035 4.724 0.719 0.3153 0.4792 2.2771
42Argon AR 42 2.171 3.352 2.458 0.5924 -0.7270 -0.6602
43Argon AR 43 1.658 3.025 1.570 1.8708 0.4716 -0.1615
44Argon AR 44 2.015 3.318 3.592 -1.1776 -2.0891 -1.6319
45Argon AR 45 1.019 4.226 0.114 -1.4335 -0.0953 -0.5499
46Argon AR 46 1.621 4.722 1.731 0.3118 0.2862 0.9394
47Argon AR 47 1.236 0.209 2.570 -0.3800 0.3034 -0.2262
48Argon AR 48 1.107 3.405 3.175 0.7078 0.6353 -0.2058
49Argon AR 49 1.036 3.980 4.023 -0.7442 0.3863 0.5171
50Argon AR 50 4.942 3.959 0.028 -0.4945 -0.5427 -0.3578
51Argon AR 51 2.750 2.001 1.596 0.2617 0.0781 -1.1608
52Argon AR 52 1.769 1.280 1.829 1.0091 -0.0491 -1.7755
53Argon AR 53 3.892 0.147 2.244 0.0665 0.3800 -0.2316
54Argon AR 54 1.322 4.776 3.451 -0.7496 -0.7912 1.4578
55Argon AR 55 0.376 1.468 3.935 -0.6509 -1.8500 -0.8614
56Argon AR 56 2.728 2.508 0.449 0.9513 1.5416 -0.5461
57Argon AR 57 1.976 1.948 0.960 0.5224 -0.5848 -0.3202
58Argon AR 58 1.479 1.402 2.795 0.0270 1.0455 0.6138
59Argon AR 59 2.326 4.300 3.837 -0.5198 1.0516 -0.3477
60Argon AR 60 1.583 1.807 4.061 0.5585 -0.0307 -1.4619
61Argon AR 61 3.630 2.633 0.831 -2.7969 0.6538 -1.5914
62Argon AR 62 2.044 2.243 2.243 -0.4373 -2.1214 2.6278
63Argon AR 63 4.021 3.213 3.358 -0.0751 1.9466 -1.6609
64Argon AR 64 2.475 1.342 3.562 -0.0774 -1.2108 0.4061
65Argon AR 65 2.641 3.753 0.327 -0.3352 1.0297 0.1584
66Argon AR 66 2.921 4.776 4.908 -0.7096 0.6935 -0.4993
67Argon AR 67 3.117 4.647 0.831 0.3148 0.2864 -0.8219
68Argon AR 68 3.055 3.628 3.135 1.7630 2.2576 0.7552
69Argon AR 69 3.159 2.021 4.795 0.7280 1.8829 0.3458
70Argon AR 70 2.079 2.608 4.588 -0.9824 0.5748 1.0455
71Argon AR 71 3.146 0.714 1.366 0.1684 -0.5257 1.2033
72Argon AR 72 3.148 3.803 1.998 0.4269 -1.2197 -0.2678
73Argon AR 73 3.051 4.715 2.822 -0.0300 -1.2029 -0.5454
74Argon AR 74 1.833 3.775 4.732 -1.2605 -0.6808 0.2866
75Argon AR 75 2.146 0.441 1.263 0.3308 -0.4730 -1.2353
76Argon AR 76 3.897 1.349 0.074 0.8640 -0.4883 -1.2810
77Argon AR 77 2.568 0.909 2.276 -1.3364 -0.5167 0.5504
78Argon AR 78 0.750 4.609 1.037 1.6011 -0.0479 0.4901
79Argon AR 79 3.895 5.063 3.489 -0.3064 -0.0822 1.2432
80Argon AR 80 0.960 1.168 4.821 1.1169 -1.3025 0.0374
81Argon AR 81 4.374 2.044 4.610 0.5650 -0.3312 -0.1887
82Argon AR 82 2.845 1.989 2.744 1.0250 -0.9478 -0.2386
83Argon AR 83 3.488 1.355 2.174 -0.7045 0.7480 -0.7522
84Argon AR 84 3.232 0.861 3.156 1.1879 -0.9798 -0.4548
85Argon AR 85 2.864 1.026 4.414 -1.0152 0.4205 -1.3106
86Argon AR 86 4.426 3.428 0.770 -0.8505 1.5544 0.3785
87Argon AR 87 3.404 2.895 2.547 -0.4559 0.2936 -0.2803
88Argon AR 88 4.603 1.115 2.034 0.6018 1.7600 -0.7041
89Argon AR 89 3.557 1.675 3.847 -0.6226 -1.2764 0.5321
90Argon AR 90 3.600 3.419 0.075 0.6881 0.2689 0.9736
91Argon AR 91 3.401 3.726 0.994 -0.6749 -0.7556 0.0629
92Argon AR 92 0.192 5.090 5.003 -0.0606 -1.0682 0.0510
93Argon AR 93 4.005 3.979 2.602 -0.6517 -1.4648 0.7342
94Argon AR 94 2.751 3.291 4.345 0.5387 0.1697 0.2571
95Argon AR 95 4.751 4.548 0.992 -1.5935 0.0305 -1.0997
96Argon AR 96 4.057 3.097 1.700 -0.1356 -0.5532 1.4938
97Argon AR 97 2.915 4.913 1.863 -0.6477 -0.2058 1.1749
98Argon AR 98 0.051 0.314 1.455 1.1463 -0.2553 -0.8920
99Argon AR 99 3.297 4.171 3.920 1.1921 -0.5417 -0.1280
100Argon AR 100 2.201 0.559 0.145 -2.1546 0.9850 -0.8281
101Argon AR 101 0.404 1.902 0.234 0.2684 1.4864 0.2678
102Argon AR 102 4.559 1.295 0.795 -0.8185 0.1854 3.4100
103Argon AR 103 4.678 4.559 2.114 -0.2692 0.4273 0.7147
104Argon AR 104 4.473 4.143 3.553 1.5132 0.6999 0.9178
105Argon AR 105 2.652 0.131 3.984 0.5066 -0.9274 0.2481
106Argon AR 106 4.582 2.308 0.634 -1.1833 -0.7555 0.5142
107Argon AR 107 3.620 1.557 1.056 -1.7076 -0.3213 -0.1657
108Argon AR 108 4.164 0.485 1.211 -0.6023 1.7699 -0.3569
109Argon AR 109 5.026 0.385 2.563 0.8574 -0.1411 -0.3869
110Argon AR 110 3.964 0.708 4.178 2.3516 -0.4632 -1.6643
111Argon AR 111 0.277 3.188 0.772 -1.5788 -1.8541 -1.1427
112Argon AR 112 4.168 2.084 1.670 0.4183 -0.6446 -1.1332
113Argon AR 113 0.614 1.006 2.078 0.3018 0.6311 -1.0163
114Argon AR 114 4.244 0.910 3.035 1.3939 -0.9413 -1.2160
115Argon AR 115 4.535 1.571 3.764 -0.2376 -1.2259 -1.2002
116Argon AR 116 4.307 0.407 0.122 -0.2502 1.7650 -0.2933
117Argon AR 117 1.214 0.252 0.313 -2.0761 -0.1607 0.1805
118Argon AR 118 4.591 2.945 2.467 -1.4596 -1.4980 0.5959
119Argon AR 119 4.101 2.120 2.835 2.4606 0.9035 0.7012
120Argon AR 120 3.740 2.689 4.154 -0.1941 -0.6392 0.4762
121Argon AR 121 3.318 0.461 0.368 0.7086 0.9908 -1.8400
122Argon AR 122 3.886 4.465 1.572 0.6610 -1.2269 -0.7330
123Argon AR 123 0.023 3.795 2.729 0.3992 -2.3672 0.3457
124Argon AR 124 4.287 3.674 4.386 0.4761 -0.8819 -0.9774
125Argon AR 125 0.185 4.445 4.270 -1.9450 0.9183 0.9863
5.10000 5.10000 5.10000
; 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 125
;Argon 2
;
; File 'mdout.mdp' was generated
; By user: spoel (500)
; On host: h140n2fls34o1123.telia.com
; At date: Thu May 8 10:57:52 2003
;
; VARIOUS PREPROCESSING OPTIONS
title = Yo
cpp = /lib/cpp
include =
define =
; RUN CONTROL PARAMETERS
integrator = md
; start time and timestep in ps
tinit = 0.0
dt = 0.002
nsteps = 100
; 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 = 0
nstvout = 0
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
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
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
epsilon_surface = 0
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
---------------------------------
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