[gmx-users] -rerun with energygrps

[Alex]

gmx check output below, not sure it's what you wanted to see...

   gmx check -s1 prod.tpr -s2 rerun_bulk.tpr

Note: When comparing run input files, default tolerances are reduced.
Reading file prod.tpr, VERSION 2018 (single precision)
Reading file rerun_bulk.tpr, VERSION 2018 (single precision)

GROMACS reminds you: "Don't Push Me, Cause I'm Close to the Edge" 
(Grandmaster Flash)

comparing inputrec
inputrec->ld_seed (-1925271974 - 339481985)
inputrec->grpopts.ngener (1 - 2)
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
grps[1].nr (1 - 2)
ngrpnr[1] (0 - 3633)
comparing flags
comparing box
comparing box_rel
comparing boxv
comparing x
comparing v


On 4/9/2018 7:12 PM, Mark Abraham wrote:
> Hi,
>
> What version is this? What does gmx compare report amwhen comparing the two
> tpr files?
>
> Mark
>
> On Mon, Apr 9, 2018, 22:54 Alex <nedomacho at gmail.com> wrote:
>
>> Hi all,
>>
>> Something funny is happening. I have a very simple system: an ion in bulk
>> TIP4P water running under OPLS-AA. mdp excerpt below:
>>
>> nstlist             =  20
>> pbc                 = xyz
>> periodic_molecules  = yes
>> ns_type             =  grid
>> rlist               =  1.0
>> coulombtype         =  pme
>> fourierspacing      =  0.135
>> rcoulomb            =  1.0
>> rvdw                =  1.0
>> vdwtype             =  cut-off
>> cutoff-scheme   = Verlet
>>
>> In order to determine ion-solvent interaction energy, i have a rerun mdp
>> that is identical to the one used for the actual simulation, but with
>>
>> energygrps = K SOL
>>
>> added. When applying gmx energy to the rerun edr, the only K-SOL options
>> are:
>>
>> 41  Coul-SR:K-SOL
>> 42  LJ-SR:K-SOL
>>
>> Nothing long-range. This has never been the case before and PME
>> contribution was always there.
>>
>> Any suggestions?
>>
>> Thank you,
>>
>> Alex
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