[gmx-users] g_energy sum

merc mertens merc.mertens at gmx.net
Mon Apr 30 10:00:11 CEST 2007


hello,

you are right but "summing" over 1 term was done only for testing purposes. first i tried to sum up all lj terms but ran into the same problem.

nevertheless i finally found the reason for the difference. the energy file is from a rerun. during the setup mdrun complained that not all frames of the trajectory used for rerunning contained velocities. therefore i reran a converted trajectory containing only the frames with velocities (i.e. only every 100th frame). the resulting energy.xvg contained 21 energy values but the sum was averaged over 2000001 steps (see below). this explains the small average value from "-sum".

this leads to the next question: was it wrong to only use the frames containing velocities in the rerun??

thanks for the help and suggestions,

merc


-------- Original-Nachricht --------
Datum: Fri, 27 Apr 2007 13:59:15 +0200
Von: "Berk Hess" <gmx3 at hotmail.com>
An: gmx-users at gromacs.org
Betreff: Re: [gmx-users] g_energy sum

> 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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