[gmx-users] g_energy sum
Erik Lindahl
lindahl at cbr.su.se
Fri Apr 27 13:41:11 CEST 2007
Hi,
If you haven't done anything special such as concatenating or cutting
the energy file in parts after the simulation, I'd say it looks like
a bug. Please create an entry at bugzilla.gromacs.org , upload the
tpr, and we'll have a look at it.
Cheers,
Erik
On Apr 27, 2007, at 1:36 PM, merc mertens wrote:
> hello,
>
> i use VERSION 3.3.1. output from
>
> g_energy -f (ener.edr) -sum -o (energy.xvg)
>
> is similar as with the "-b 2000" flag:
>
> Statistics over 2000001 steps [ 0.0000 thru 4000.0000 ps ], 1 data
> sets
>
> Energy Average RMSD Fluct.
> Drift Tot-Drift
> ----------------------------------------------------------------------
> ---------
> Coul-SR:Protein-trna -0.0237376 5.19622 0
> 0.0118159 47.2635
> Total -0.0237376 -- --
> -- --
>
> in comparison from the xvg:
>
> @ s0 legend "Coul-SR:Protein-trna"
> @ s1 legend "Sum"
> 0.000000 -1107.173950
> 100.000000 -1201.496948
> 200.000000 -1142.097778
> 300.000000 -1082.942383
> 400.000000 -1063.810547
> 500.000000 -1058.372314
> 600.000000 -1061.625488
> 700.000000 -1326.301270
> 800.000000 -1233.008667
> 900.000000 -1169.119751
> 1000.000000 -1082.796021
> 1100.000000 -1261.529175
> 1200.000000 -1257.951904
> 1300.000000 -1310.429565
> 1400.000000 -1251.131592
> 1500.000000 -1235.889893
> 1600.000000 -1233.731201
> 1700.000000 -1077.790649
> 1800.000000 -1134.157471
> 1900.000000 -1231.017334
> 2000.000000 -1171.813721
> 2100.000000 -1311.884399
> 2200.000000 -1142.125366
> 2300.000000 -1169.552979
> 2400.000000 -1205.442383
> 2500.000000 -1189.931519
> 2600.000000 -1148.712402
> 2700.000000 -1003.882751
> 2800.000000 -1104.013794
> 2900.000000 -1076.985474
> 3000.000000 -1131.902832
> 3100.000000 -1135.494995
> 3200.000000 -1080.656250
> 3300.000000 -1257.183594
> 3400.000000 -1138.595215
> 3500.000000 -1107.039062
> 3600.000000 -1051.498657
> 3700.000000 -1139.150391
> 3800.000000 -1070.984741
> 3900.000000 -1186.214600
> 4000.000000 -1129.730713
>
> i think that the ener.edr only should contain only those steps
> listed in the xvg.
>
> cheers,
> merc
>
>
> -------- Original-Nachricht --------
> Datum: Fri, 27 Apr 2007 13:04:04 +0200
> Von: Erik Lindahl <lindahl at cbr.su.se>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Betreff: Re: [gmx-users] g_energy sum
>
>> Oops,
>>
>> Sometimes it helps to read the mail. Mea culpa - forget my previous
>> answer, this is something else.
>>
>> It could simply be a bug in g_energy; which version are you using,
>> and what do you get if you remove "-b 2000" (i.e. include all steps)?
>>
>> Cheers,
>>
>> Erik
>>
>> On Apr 27, 2007, at 12:24 PM, merc mertens wrote:
>>
>>> hello,
>>>
>>> when i calculate energies with
>>>
>>> g_energy -f (ener.edr) -b 2000 -sum -o (energy.xvg)
>>>
>>> e.g. i get this average in the log:
>>>
>>> Statistics over 1000001 steps [ 2000.0000 thru 4000.0000 ps ], 1
>>> data sets
>>>
>>> Energy Average RMSD Fluct.
>>> Drift Tot-Drift
>>> --------------------------------------------------------------------
>>> --
>>> ---------
>>> Coul-SR:Protein-trna -0.0239528 0 0
>>> 0.0381909 76.3818
>>> Total -0.0239528 -- --
>>> -- --
>>>
>>>
>>> but i get this in the output energy.xvg:
>>>
>>> @ s0 legend "Coul-SR:Protein-trna"
>>> @ s1 legend "Sum"
>>> 2000.000000 -1171.813721
>>> 2100.000000 -1311.884399
>>> 2200.000000 -1142.125366
>>> 2300.000000 -1169.552979
>>> 2400.000000 -1205.442383
>>> 2500.000000 -1189.931519
>>> 2600.000000 -1148.712402
>>> 2700.000000 -1003.882751
>>> 2800.000000 -1104.013794
>>> 2900.000000 -1076.985474
>>> 3000.000000 -1131.902832
>>> 3100.000000 -1135.494995
>>> 3200.000000 -1080.656250
>>> 3300.000000 -1257.183594
>>> 3400.000000 -1138.595215
>>> 3500.000000 -1107.039062
>>> 3600.000000 -1051.498657
>>> 3700.000000 -1139.150391
>>> 3800.000000 -1070.984741
>>> 3900.000000 -1186.214600
>>> 4000.000000 -1129.730713
>>>
>>> the average energies from the log and the xvg do not match. does
>>> anybody know what is wrong here?
>>> thank you in advance,
>>>
>>> merc
>>> --
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