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" <[EMAIL PROTECTED]> An: gmx-users@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 <[EMAIL PROTECTED]> > >Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org> > >To: Discussion list for GROMACS users <gmx-users@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 <[EMAIL PROTECTED]> > >>An: Discussion list for GROMACS users <gmx-users@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 > >>>>-- > >>>>"Feel free" - 10 GB Mailbox, 100 FreeSMS/Monat ... > >>>>Jetzt GMX TopMail testen: http://www.gmx.net/de/go/topmail > >>>>_______________________________________________ > >>>>gmx-users mailing list gmx-users@gromacs.org > >>>>http://www.gromacs.org/mailman/listinfo/gmx-users > >>>>Please search the archive at http://www.gromacs.org/search before > >>>>posting! > >>>>Please don't post (un)subscribe requests to the list. Use the > >>>>www interface or send it to [EMAIL PROTECTED] > >>>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>> > >>>_______________________________________________ > >>>gmx-users mailing list gmx-users@gromacs.org > >>>http://www.gromacs.org/mailman/listinfo/gmx-users > >>>Please search the archive at http://www.gromacs.org/search before > >>>posting! > >>>Please don't post (un)subscribe requests to the list. Use the > >>>www interface or send it to [EMAIL PROTECTED] > >>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > >>-- > >>"Feel free" - 10 GB Mailbox, 100 FreeSMS/Monat ... > >>Jetzt GMX TopMail testen: http://www.gmx.net/de/go/topmail > >>_______________________________________________ > >>gmx-users mailing list gmx-users@gromacs.org > >>http://www.gromacs.org/mailman/listinfo/gmx-users > >>Please search the archive at http://www.gromacs.org/search before > >>posting! > >>Please don't post (un)subscribe requests to the list. Use the > >>www interface or send it to [EMAIL PROTECTED] > >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > >_______________________________________________ > >gmx-users mailing list gmx-users@gromacs.org > >http://www.gromacs.org/mailman/listinfo/gmx-users > >Please search the archive at http://www.gromacs.org/search before > posting! > >Please don't post (un)subscribe requests to the list. Use the www > interface > >or send it to [EMAIL PROTECTED] > >Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _________________________________________________________________ > Live Search, for accurate results! http://www.live.nl > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. 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