GROMACS version: 2019.1
GROMACS modification: No
Hi,
I’ve been trying to use Polarization in Gromacs 2019.1. I am working on an ionic liquid system of a 100 pairs and I am using the CL&P forcefield. The melting temperature of the simulated liquid was higher than the expected one, so I tried scaling it down by a factor of 0.8 but the effects that occurred were not the desired ones. Hence, the consideration of polarization which seemed promising at first. I made the required edits of the topology files adding the shell particles and the [polarization ]field. I changed the parameter files following the requirements of previous literature (pasted at the end) , but I keep getting the same error message:
step 0: EM did not converge in 50 iterations, RMS force 9.43e+00
step 1: EM did not converge in 50 iterations, RMS force 9.43e+00
step 2: EM did not converge in 50 iterations, RMS force 9.43e+00
step 3: EM did not converge in 50 iterations, RMS force 9.44e+00
step 4: EM did not converge in 50 iterations, RMS force 9.46e+00
step 5: EM did not converge in 50 iterations, RMS force 9.48e+00
step 6: EM did not converge in 50 iterations, RMS force 9.50e+00
step 7: EM did not converge in 50 iterations, RMS force 9.53e+00
step 8: EM did not converge in 50 iterations, RMS force 9.57e+00
step 9: EM did not converge in 50 iterations, RMS force 9.61e+00
step 10: EM did not converge in 50 iterations, RMS force 9.66e+00
step 11: EM did not converge in 50 iterations, RMS force 9.73e+00
step 12: EM did not converge in 50 iterations, RMS force 9.80e+00
step 13: EM did not converge in 50 iterations, RMS force 9.89e+00
step 14: EM did not converge in 50 iterations, RMS force 9.99e+00
step 15: EM did not converge in 50 iterations, RMS force 1.01e+01
step 16: EM did not converge in 50 iterations, RMS force 1.03e+01
step 17: EM did not converge in 50 iterations, RMS force 1.05e+01
step 18: EM did not converge in 50 iterations, RMS force 1.08e+01
step 19: EM did not converge in 50 iterations, RMS force 1.12e+01
step 20: EM did not converge in 50 iterations, RMS force 1.20e+01
[scc2:01514] *** Process received signal ***
[scc2:01514] Signal: Floating point exception (8)
[scc2:01514] Signal code: Floating point overflow (4)
[scc2:01514] Failing at address: 0x7f2525a867a8
[scc2:01514] [ 0] /lib64/libpthread.so.0(+0xf5f0)[0x7f25239dd5f0]
[scc2:01514] [ 1] /share/pkg.7/gromacs/2019.1/install/bin/…/lib64/libgromacs_mpi.so.4(+0x10ea7a8)[0x7f2525a867a8]
[scc2:01514] [ 2] /share/pkg.7/gromacs/2019.1/install/bin/…/lib64/libgromacs_mpi.so.4(+0x10ed83e)[0x7f2525a8983e]
[scc2:01514] [ 3] /share/pkg.7/gromacs/2019.1/install/bin/…/lib64/libgromacs_mpi.so.4(_Z14spread_on_gridPK9gmx_pme_tPK14pme_atomcomm_tPK10pmegrids_tbbPfbi+0x15f)[0x7f2525a893fe]
[scc2:01514] [ 4] /share/pkg.7/gromacs/2019.1/install/bin/…/lib64/libgromacs_mpi.so.4(_Z10gmx_pme_doP9gmx_pme_tiiPA3_fS2_PfS3_S3_S3_S3_S3_S2_PK9t_commreciiP6t_nrnbP13gmx_wallcycleS2_S2_S3_S3_ffS3_S3_i+0x6e6)[0x7f2525a6af97]
[scc2:01514] [ 5] /share/pkg.7/gromacs/2019.1/install/bin/…/lib64/libgromacs_mpi.so.4(Z17do_force_lowlevelP10t_forcerecPK10t_inputrecPK6t_idefPK9t_commrecPK14gmx_multisim_tP6t_nrnbP13gmx_wallcyclePK9t_mdatomsPA3_fP9history_tSL_PN3gmx15ForceWithVirialEP14gmx_enerdata_tP8t_fcdataSL_P8t_lambdaPfPK7t_graphPK8t_blockaSL_iSX+0x1092)[0x7f252549ee3b]
[scc2:01514] [14] /share/pkg.7/gromacs/2019.1/install/bin/…/lib64/libgromacs_mpi.so.4(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x38a)[0x7f2524fffbd6]
[scc2:01514] [15] gmx_mpi[0x40b593]
[scc2:01514] [16] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f2523622505]
[scc2:01514] [17] gmx_mpi[0x40b439]
[scc2:01514] *** End of error message ***
Floating point exception
The constant pressure equilibration parameter file:
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.001
nsteps = 10000
comm-mode = linear
nstcomm = 100
comm-grps = System
; OUTPUT CONTROL OPTIONS
nstxout = 1000
nstvout = 1000
nstfout = 1000
; Output frequency for energies to log file and energy file
nstlog = 100
nstcalcenergy = 1
nstenergy = 100
; NEIGHBORSEARCHING PARAMETERS
cutoff-scheme = verlet
nstlist = 1
ns-type = Grid
pbc = xyz
rlist = 1.2
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = PME
rcoulomb = 1.2
vdwtype = cutoff
vdw-modifier = potential-switch
rvdw-switch = 1.0
rvdw = 1.2
DispCorr = EnerPres
; TEMPERATURE COUPLING
tcoupl = V-rescale
; Groups to couple separately
tc-grps = System
tau-t = 0.1
ref-t = 240
; PRESSURE COUPLING IS NOT YET SUPPORTED
pcoupl = Berendsen
pcoupltype = isotropic
tau-p = 1.0
ref-p = 1.0
compressibility = 4.5e-5
; GENERATE VELOCITIES FOR STARTUP RUN, OTHERWISE DO
; NOT GENERATE NEW VELOCITIES IF PREVIOUSLY EQUILIBRATED
gen-vel = yes
gen-temp = 240
gen-seed = -1
; OPTIONS FOR BONDS
constraints = h-bonds ; can also be h-bonds, not all-bonds
continuation = no
; Drude Parameters
emtol = 1.0
niter = 50
Can you point me in the right direction?
Thanks for your help!