Re: [gmx-users] -rerun with energygrps
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 Alexwrote: 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] -rerun with energygrps
This is 2018, I will compare later. The issue is mostly sort of solved, as I just moved all of electrostatics to 'cut-off' with a large radius for the rerun. I first thought it was because the system was not neutral (ion + water without the counterion, so it refused to report the PME part), but same behavior with a counterion. It would be interesting to see if you guys could independently reproduce this with me supplying just the mdp files. Just a 3x3x3 box with a single K+ ion and TIP4P water. em followed by 1 ns NPT (Berendsen) relax, followed by 10 ns NPT production test. Alex 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 Alexwrote: 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] -rerun with energygrps
Hi, What version is this? What does gmx compare report amwhen comparing the two tpr files? Mark On Mon, Apr 9, 2018, 22:54 Alexwrote: > 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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] -rerun with energygrps
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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.