Hi, I'm using gromacs 4.5.4 and I've got a detailed question on how the mass weighting works.
Given a trajectory and a pdb from http://code.google.com/p/mdanalysis/source/browse/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb http://code.google.com/p/mdanalysis/source/browse/testsuite/MDAnalysisTests/data/adk_oplsaa.trr I called the following structure="adk_oplsaa.pdb" trajectory="adk_oplsaa.trr" g_rms -s $structure -f $trajectory -o d_rmsd.xvg << EOF 3 3 EOF g_rms -nomw -s $structure -f $trajectory -o d_rmsd_nomw.xvg << EOF 3 3 EOF I was expecting the RMSD values to be identical: all the CA atoms have identical weights with the -mw flag on, which (to my mind) should be yield same results to when -nomw is specified and the same set of atoms is selected. The question: is this an unreasonable expectation? sdiff d_rmsd.xvg d_rmsd_nomw.xvg | tail # consistent only for 5 sig figs 0.0000000 0.0000369 | 0.0000000 0.0000368 100.0000076 0.9818456 | 100.0000076 0.9818469 200.0000153 0.8223789 | 200.0000153 0.8223798 300.0000000 0.6450028 | 300.0000000 0.6450034 400.0000305 0.8285408 | 400.0000305 0.8285414 500.0000305 1.9386379 | 500.0000305 1.9386411 600.0000000 1.6888058 | 600.0000000 1.6888076 700.0000610 1.6885630 | 700.0000610 1.6885644 800.0000610 1.8211102 | 800.0000610 1.8211110 900.0000610 2.1306074 | 900.0000610 2.1306095 (BTW, the g_rms -h mentions something about a '-debug flag' but it seems not to be working.) As a check, I've used MDAnalysis 0.7.6-devel (http://mdanalysis.googlecode.com) and the following code to get RMSD on the same data, which was consistent over 14 sig figs. from MDAnalysis import * from MDAnalysis.analysis.align import * conf = "adk_oplsaa.pdb" traj = "adk_oplsaa.trr" ref = Universe(conf) mob = Universe(conf, traj) rms_fit_trj(mob, ref, select="name CA", rmsdfile="rmsd.dat", mass_weighted=True) rms_fit_trj(mob, ref, select="name CA", rmsdfile="rmsd_nomw.dat", mass_weighted=False) sdiff rmsd.dat rmsd_nomw.dat # consistent over 14 sig figs 3.686669177327545608e-04 | 3.686671021799712840e-04 9.818467126090068220e+00 | 9.818467126090039798e+00 8.223796870415890581e+00 8.223796870415890581e+00 6.450033517100112412e+00 | 6.450033517100091096e+00 8.285414822442923821e+00 | 8.285414822442906058e+00 1.938640271585943964e+01 | 1.938640271585941832e+01 1.688807649241958941e+01 | 1.688807649241956454e+01 1.688564785098214571e+01 | 1.688564785098212795e+01 1.821111456215330549e+01 | 1.821111456215327706e+01 2.130609827021595137e+01 | 2.130609827021593006e+01 Thanks for helping me figure it out guys, Jan -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
