Archive from user: Chris Neale I created a system with two magnesium ions. Used the -DMG\_ALLNER option in the .mdp file (or not) to get different MG parameters with the charmm36 force field from MacKerell’s site. The two .tpr files do indeed differ, but gmx check -s1 -s2 does not notice this. All tested in gmx 5.1.2. \#\#\# There is a difference in these two .tpr files: $ gmx dump -s regmg.tpr >z.reg $ gmx dump -s allnermg.tpr >z.allner $ diff z.reg z.allner 1c1 < regmg.tpr: --- > allnermg.tpr: 12c12 < ld-seed = 3435682522 --- > ld-seed = 2505241084 190c190 < functype[0]=LJ_SR, c6= 2.22434992e-05, c12= 1.97089389e-09 --- > functype[0]=LJ_SR, c6= 2.23024417e-05, c12= 1.00746762e-08 3822c3822 < type[0]={name="MG",nameB="MG"} --- > type[0]={name="MGA",nameB="MGA"} \#\#\#\#\# But gmx check -s –2 doesn’t pick it up: $ gmx check -s1 regmg.tpr -s2 allnermg.tpr Reading file regmg.tpr, VERSION 5.1.2 (single precision) Reading file allnermg.tpr, VERSION 5.1.2 (single precision) comparing inputrec inputrec->ld_seed (3435682522 - 2505241084) comparing top comparing idef comparing ilist BONDS comparing ilist G96BONDS comparing ilist MORSE comparing ilist CUBICBONDS comparing ilist CONNBONDS comparing ilist HARMONIC comparing ilist FENEBONDS comparing ilist TABBONDS comparing ilist TABBONDSNC comparing ilist RESTRAINTPOT comparing ilist ANGLES comparing ilist G96ANGLES comparing ilist RESTRANGLES comparing ilist LINEAR_ANGLES comparing ilist CROSS_BOND_BOND comparing ilist CROSS_BOND_ANGLE comparing ilist UREY_BRADLEY comparing ilist QANGLES comparing ilist TABANGLES comparing ilist PDIHS comparing ilist RBDIHS comparing ilist RESTRDIHS comparing ilist CBTDIHS comparing ilist FOURDIHS comparing ilist IDIHS comparing ilist PIDIHS comparing ilist TABDIHS comparing ilist CMAP comparing ilist GB12 comparing ilist GB13 comparing ilist GB14 comparing ilist GBPOL comparing ilist NPSOLVATION comparing ilist LJ14 comparing ilist COUL14 comparing ilist LJC14_Q comparing ilist LJC_NB comparing ilist LJ_SR comparing ilist BHAM comparing ilist LJ_LR comparing ilist BHAM_LR comparing ilist DISPCORR comparing ilist COUL_SR comparing ilist COUL_LR comparing ilist RF_EXCL comparing ilist COUL_RECIP comparing ilist LJ_RECIP comparing ilist DPD comparing ilist POLARIZATION comparing ilist WATERPOL comparing ilist THOLE comparing ilist ANHARM_POL comparing ilist POSRES comparing ilist FBPOSRES comparing ilist DISRES comparing ilist DISRESVIOL comparing ilist ORIRES comparing ilist ORDEV comparing ilist ANGRES comparing ilist ANGRESZ comparing ilist DIHRES comparing ilist DIHRESVIOL comparing ilist CONSTR comparing ilist CONSTRNC comparing ilist SETTLE comparing ilist VSITE2 comparing ilist VSITE3 comparing ilist VSITE3FD comparing ilist VSITE3FAD comparing ilist VSITE3OUT comparing ilist VSITE4FD comparing ilist VSITE4FDN comparing ilist VSITEN comparing ilist COM_PULL comparing ilist EQM comparing ilist EPOT comparing ilist EKIN comparing ilist ETOT comparing ilist ECONS comparing ilist TEMP comparing ilist VTEMP comparing ilist PDISPCORR comparing ilist PRES comparing ilist DH/DL_CON comparing ilist DV/DL comparing ilist DK/DL comparing ilist DVC/DL comparing ilist DVV/DL comparing ilist DVB/DL comparing ilist DVR/DL comparing ilist DVT/DL comparing atoms comparing block cgs comparing block mols comparing blocka excls comparing groups comparing flags comparing box comparing box_rel comparing boxv comparing x comparing v gcq#401: "It's easy to remember: a half a kT is equal to five fourths of a kJ/mol." (Anders Gabrielsson) *(from redmine: issue id 2024, created on 2016-08-04 by gmxdefault, closed on 2017-12-20)* * Changesets: * Revision fc0b6a720137828e1071799526d918947494e9c2 by Erik Lindahl on 2017-12-19T00:57:18Z: ``` Use reduced default tolerances for tpx comparison The tolerances for gmx check are mainly intended for handling slight statistical deviations, but they can hide differences between tpr files, when the user likely wants exact checks. This changes changes the default relative tolerance to 0.000001 and the absolute tolerance to zero, so that we only allow for minor differences due to compiler optimization. Fixes #2024. Change-Id: I55b882a194d931bf5c36541e25339b6e1eb0a1e4 ``` * Uploads: * [allnermg.tpr](/uploads/90ebcadbaf1d58513f4855ea4a80863a/allnermg.tpr) * [regmg.tpr](/uploads/de2d4428c378b10c23504e52d47ac2fe/regmg.tpr)