[gmx-users] R: problem with .edr file
Anna Marabotti
anna.marabotti at isa.cnr.it
Tue Sep 14 09:31:09 CEST 2010
Dear Berk,
probably I was not able to explain correctly my problem. I can assure you
that the problem with .edr file exists, and that using that .edr file I'm
not able to create graphs in which I can see the behaviour of the energy as
I usually did in other simulations.
To be more clear, I'm pasting here one of the incorrect .xvg files I
obtained from the "bad" .edr file during my last simulations:
# This file was created Thu Sep 9 09:50:11 2010
# by the following command:
# g_energy -f FAPP2-GLTPapo_md20ns1.edr -s FAPP2-GLTPapo_md20ns1.tpr -o
FAPP2-GLTPapo_md20ns1_ene.xvg
#
# g_energy is part of G R O M A C S:
#
# Gnomes, ROck Monsters And Chili Sauce
#
@ 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 "Potential"
@ s1 legend "Kinetic En."
@ s2 legend "Total Energy"
@ s3 legend "Temperature"
@ s4 legend "Pressure (bar)"
120.000008 -705703.875000 135419.265625 -570284.625000 315.046173
29.590607
200.000015 -705340.625000 133275.937500 -572064.687500 310.059814
-2.463196
300.000000 -708394.437500 133758.062500 -574636.375000 311.181458
83.616455
400.000031 -705674.062500 133148.625000 -572525.437500 309.763611
184.007294
20120.000000 -707719.500000 133799.937500 -573919.562500 311.278870
-21.107380
(and tha'ts all, between 400 and 20120 there are NO steps saved at all).
This one, instead, is the one I obtained from the "good" .edr file obtained
by the mdrun -rerun command using the same .trr file produced together with
the "bad" .edr file:
# This file was created Fri Sep 10 14:29:00 2010
# by the following command:
# g_energy -f provareruns1.edr -s FAPP2-GLTPapo_md20ns1.tpr -o
provareruns1-ene.xvg
#
# g_energy is part of G R O M A C S:
#
# GROup of MAchos and Cynical Suckers
#
@ 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 "Potential"
@ s1 legend "Kinetic En."
@ s2 legend "Total Energy"
@ s3 legend "Temperature"
@ s4 legend "Pressure (bar)"
200.000015 -705339.687500 133179.312500 -572160.375000 309.835022
14.314774
300.000000 -708398.312500 133782.171875 -574616.125000 311.237518
80.675186
400.000031 -705675.687500 133066.015625 -572609.687500 309.571442
199.023102
500.000031 -707683.750000 133367.000000 -574316.750000 310.271667
-76.453644
600.000000 -707483.875000 133314.359375 -574169.500000 310.149200
-52.654724
700.000061 -707307.562500 131717.437500 -575590.125000 306.434052
-11.840759
800.000061 -707477.500000 132927.453125 -574550.062500 309.249084
26.638367
900.000061 -705743.500000 134276.265625 -571467.250000 312.387024
33.967567
1000.000061 -708540.812500 132236.125000 -576304.687500 307.640747
119.255417
1100.000000 -707124.625000 132218.968750 -574905.625000 307.600800
155.241943
1200.000000 -706612.875000 133102.171875 -573510.687500 309.655548
43.426445
1300.000122 -706655.187500 133461.312500 -573193.875000 310.491119
17.628586
1400.000122 -706465.375000 133988.359375 -572477.000000 311.717255
-46.493118
1500.000122 -707033.312500 133896.250000 -573137.062500 311.502930
81.037834
1600.000122 -705532.000000 133472.796875 -572059.187500 310.517792
-59.871452
1700.000122 -707517.750000 133351.031250 -574166.750000 310.234497
-86.916000
1800.000122 -707692.375000 133077.031250 -574615.375000 309.597046
-107.954300
1900.000122 -709641.750000 132820.000000 -576821.750000 308.999115
-31.007534
2000.000122 -706855.937500 133823.843750 -573032.125000 311.334503
58.357574
2100.000000 -708052.062500 133547.406250 -574504.625000 310.691376
54.303329
2200.000000 -708555.875000 133606.718750 -574949.125000 310.829315
-60.939171
2300.000000 -706562.000000 134384.609375 -572177.375000 312.639099
50.716835
2400.000000 -707270.125000 133340.296875 -573929.812500 310.209564
-8.514526
2500.000000 -708014.500000 133456.546875 -574557.937500 310.479950
8.023079
2600.000244 -706436.000000 133169.718750 -573266.250000 309.812714
13.177231
2700.000244 -707959.125000 133542.062500 -574417.062500 310.678925
73.762177
2800.000244 -707810.187500 133236.718750 -574573.500000 309.968597
115.054741
2900.000244 -706490.187500 133106.140625 -573384.062500 309.664795
-90.756798
3000.000244 -709224.000000 132905.625000 -576318.375000 309.198303
-65.078964
3100.000244 -705765.250000 133043.562500 -572721.687500 309.519196
2.774910
3200.000244 -710229.375000 133819.562500 -576409.812500 311.324585
-23.851131
3300.000244 -706552.062500 134060.343750 -572491.750000 311.884705
-1.245949
3400.000244 -708047.250000 132793.031250 -575254.250000 308.936371
67.046944
3500.000244 -706934.750000 133241.578125 -573693.187500 309.979858
-19.809002
3600.000244 -705629.812500 133803.093750 -571826.750000 311.286224
156.413666
3700.000244 -707516.187500 134178.500000 -573337.687500 312.159607
-64.707054
3800.000244 -709205.875000 133771.171875 -575434.687500 311.211945
-24.293491
3900.000244 -707249.687500 132882.812500 -574366.875000 309.145233
-31.814121
4000.000244 -706485.062500 132661.171875 -573823.875000 308.629578
55.151711
4100.000000 -707033.375000 133012.593750 -574020.750000 309.447144
81.014641
4200.000000 -706742.812500 132059.484375 -574683.312500 307.229797
-26.515224
4300.000000 -709319.375000 133830.562500 -575488.812500 311.350098
29.891098
4400.000000 -707927.312500 133677.281250 -574250.000000 310.993530
135.107056
4500.000000 -705877.812500 133892.250000 -571985.562500 311.493622
9.522690
4600.000000 -709040.437500 133866.609375 -575173.812500 311.433990
-5.468666
4700.000000 -707885.375000 132698.843750 -575186.500000 308.717255
-77.259377
4800.000000 -709289.250000 133927.406250 -575361.875000 311.575409
-82.923164
4900.000000 -707531.500000 132883.781250 -574647.750000 309.147522
144.439972
5000.000000 -708285.687500 133118.156250 -575167.500000 309.692780
-99.921867
(it continues up to 20000 with all the steps)
It is evident that the information contained in the "bad" .edr file is not
the same as the one contained in the "good" .edr file, but both derived from
the same .trr file, so I think that the problem is not the simulation itself
but the way in which the .edr file was saved. At present, I cannot solve the
problem installing the version 4.5, but since it is the first time that I
have this problem, I wonder why it happened. Could you (or anybody else)
help me to understand it?
Thank you very much
Anna
------------------------------
Date: Mon, 13 Sep 2010 19:36:31 +0200
From: Berk Hess <gmx3 at hotmail.com>
Subject: RE: [gmx-users] problem with .edr file
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <COL113-W203313D1D0D01C0C67CB3E8E770 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
There is no problem at all and you only got notices, not errors.
In Gromacs version 4.0 and before each frame in an energy file always
contained the energy averages
over the whole simulation up to the current step. For proper checkpointing
we therefore had to write
an energy energy file frame every time a checkpoint is written. The frames
cause no problems and all,
and g_energy ignores them by default.
Starting with version 4.5 energy frames only contain the average starting
from the time when the previous
frame was written and we could get rid of the inelegant (bug harmless) extra
frames.
Note that the energy file that you obtained from the rerun does not have the
exact averages and fluctuations
with statistics over all md steps.
Berk
Date: Mon, 13 Sep 2010 09:59:43 +0200
From: anna.marabotti at isa.cnr.it
To: gmx-users at gromacs.org
Subject: [gmx-users] problem with .edr file
Dear
gmx-users,
I launched several
dynamics with gromacs 4.0.7, they finished regularly with apparently no
problems
(=no error messages at the end of the runs), but when I started analyzing
the
results, I found a problem in the .edr files. In details, when I used them
with
g_energy, I found that only 4 of the points that should have been saved as I
stated in the .mdp file ( I set to save energy, force, coordinates, log
every
100 ps) were present in the file. The .log files were correct and I can see
energies in all the steps. I checked both the .trr and the .edr files with
gmxcheck and I found that the .trr (and also the .xtc) files were correct,
whereas the .edr files gave me the following message error:
Checking energy file
FAPP2-GLTPapo_md20ns1.edr
Opened FAPP2-GLTPapo_md20ns1.edr as single
precision energy file
frame: 60000 (index
0), t: 120.000
Reading energy
frame 2 time 300.000
Timesteps at t=200
don't match (80, 100)
Reading energy frame 200 time
20100.000
Timesteps at t=20100 don't match (100, 20)
Last energy frame
read 201 time 20120.000
Found 202 frames.
I used mdrun -rerun
and the .trr file to obtain a new .edr file, and this time the file was
correct,
with all the points present, so I think that the run was made correctly, but
the
.edr was not properly saved. I don't know why this happened: do you think it
could be a problem in the Gromacs version, or in the Gromacs installation?
Any
hint will be very appreciated.
Many thanks in
advance and best regards
Anna
____________________________________________________
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and
Computational Biology
Institute of Food Science,
CNR
Via Roma, 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Email: anna.marabotti at isa.cnr.it
Skype account: annam1972
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
"If you think you are too small to make
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