gmx check does not notice difference in .tpr files that differ only in LJ parameters - Redmine #2024
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 fc0b6a72 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: