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!