[gmx-users] [Fwd: creation of edr files in mdrun]
Sidney Elmer
sidnasty at stanford.edu
Wed Jan 15 01:28:01 CET 2003
Sorry about that, I forgot to attach the energy.xvg file.
Sidney Elmer wrote:
> I am using gromacs3.1.3. Is there a known bug or problem creating the
> edr file with mdrun? The size of the file increases exponentially the
> longer the simulation runs. And when I use g_energy, there are multiple
>
> entries for a given time point. Initially, there is just one entry,
> then it increass to three, then five, etc. For long runs, the size of
> my edr file becomes exorbitantly large. Here is an example of the
> output of g_energy. Specifically, notice that at 3260ps there starts to
>
> be triplicate entries offset by +/- dt~0.002ps. Then, at 6520ps, five
> entries are printed at offsets of dt ~0.002ps, again. At similar
> increments (3260ps), the number of entries increases to seven, then
> nine, then
> eleven, etc. Before long, my file is huge due to all these duplicate
> entries. Thanks.
>
> Sid
-------------- next part --------------
# This file was created by g_energy
# which is part of G R O M A C S:
# GROup of MAchos and Cynical Suckers
# All this happened at: Mon Jan 13 14:55:40 2003
#
@ title "Gromacs Energies"
@ xaxis label "Time (ps)"
@ yaxis label "E (kJ mol\S-1\N)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "LJ (SR)"
0.000000 -4.734968
10.000000 -4.728019
20.000000 -4.646712
30.000002 -4.464443
40.000000 -4.474265
50.000004 -4.362068
60.000004 -4.743793
70.000000 -4.338681
80.000000 -4.540112
90.000008 -4.719812
100.000008 -4.476414
-- snip --
3200.000000 -4.691115
3210.000000 -4.893755
3220.000000 -4.984208
3230.000000 -4.454930
3240.000000 -4.512129
3250.000000 -4.572662
3259.998047 -4.603794
3260.000000 -4.592428
3260.001953 -4.583927
3269.998047 -4.632971
3270.000000 -4.633756
3270.001953 -4.629097
3279.998047 -4.687802
3280.000000 -4.704625
3280.001953 -4.721792
3289.998047 -4.491456
3290.000000 -4.468472
3290.001953 -4.454946
3299.998047 -4.610930
3300.000000 -4.607373
3300.001953 -4.601793
3309.998047 -4.599342
3310.000000 -4.609614
3310.001953 -4.625542
3319.998047 -4.507868
3320.000000 -4.510793
3320.001953 -4.517689
3329.998047 -4.700677
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3330.001953 -4.735167
3339.998047 -4.624229
3340.000000 -4.629624
3340.001953 -4.637604
3349.998047 -4.537808
3350.000000 -4.551056
3350.001953 -4.575131
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3360.000000 -4.553988
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3369.998047 -4.715950
3370.000000 -4.707399
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3380.000000 -4.667457
3380.001953 -4.675247
3389.998047 -4.794401
3390.000000 -4.784310
3390.001953 -4.773669
-- snip --
6399.998047 -4.674603
6400.000000 -4.658774
6400.001953 -4.643170
6409.998047 -4.935017
6410.000000 -4.959487
6410.001953 -4.976921
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6500.001953 -4.562204
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6539.998047 -4.741010
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6540.003906 -4.775233
6549.996094 -4.767949
6549.998047 -4.772144
6550.000000 -4.771480
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6550.003906 -4.748351
6559.996094 -4.907051
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6640.000000 -4.585169
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6640.003906 -4.602885
-- snip --
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