[gmx-users] g_energy sum
Berk Hess
gmx3 at hotmail.com
Fri Apr 27 13:59:15 CEST 2007
Hi,
Well there is something special, in the sense that the sum is over
just one term, so summing does not make much sense.
But also in that case it should work.
Berk.
>From: Erik Lindahl <lindahl at cbr.su.se>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] g_energy sum
>Date: Fri, 27 Apr 2007 13:41:11 +0200
>
>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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>>>
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