[gmx-users] KCl forms crystals at c=0.15M with amber99sb-ildn

[Daniel Bauer]

Hello,


We are trying to use amber99sb-ildn with gromacs2018.1 for simulations
of a protein in a salt solution. However, we observed that KCl seems to
form stable salt crystals even at concentrations as low as 0.15 mol/l at
T=298K in our system. Our MDP options have been taken from
10.5281/zenodo.1010238 and are listed below. It is reproducible with a
system containing only 6000 TIP3P water molecules and 16 KCl (0.15M),
generated by:

gmx genconf -f spc216.gro -o waterbox.gro -nbox 3 3 3

gmx grompp -f genions -c waterbox -o genions

gmx genion -nname CL -pname K -conc 0.15 -s genions -p topol.top


Does someone have an explanation what might cause this to happen? Our
MDP options are listed below and an RDF showing the accumulation is
attached.


Best Regards,

Daniel


Command line:
;      gmx grompp -f md.mdp -c em/em -o md/md.tpr

; RUN CONTROL PARAMETERS
integrator               = md
tinit                    = 0
dt                       = 0.002
nsteps                   = 1250000
init-step                = 0
simulation-part          = 1
comm-mode                = Linear
nstcomm                  = 1
comm-grps                = System

; NEIGHBORSEARCHING PARAMETERS
cutoff-scheme            = Verlet
nstlist                  = 10
ns-type                  = Grid
pbc                      = xyz
periodic-molecules       = no
verlet-buffer-tolerance  = 0.005
rlist                    = 1.0

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = pme
coulomb-modifier         = Potential-shift-Verlet
rcoulomb-switch          = 0
rcoulomb                 = 1.0
epsilon-r                = 1
epsilon-rf               = 0
vdw-type                 = Cut-off
vdw-modifier             = Potential-shift-Verlet
; cut-off lengths      
rvdw-switch              = 0
rvdw                     = 1.0
DispCorr                 = EnerPres
table-extension          = 1
energygrp-table          =
fourierspacing           = 0.12
fourier-nx               = 0
fourier-ny               = 0
fourier-nz               = 0
pme-order                = 4
ewald-rtol               = 1e-05
ewald-rtol-lj            = 0.001
lj-pme-comb-rule         = Geometric
ewald-geometry           = 3d
epsilon-surface          = 0

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling 
tcoupl                   = V-rescale
nsttcouple               = -1
nh-chain-length          = 10
tc-grps                  = System
tau_t                    = 0.1
ref-t                    = 298.0

; pressure coupling    
Pcoupl                   = Berendsen
Pcoupltype               = isotropic
nstpcouple               = -1
tau_p                    = 4.0
compressibility          = 4.5e-5
ref_p                    = 1.0
refcoord_scaling         = all

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = yes
gen_temp                 = 298.0
gen_seed                 = -1

; OPTIONS FOR BONDS   
constraints              = all-bonds
constraint_algorithm     = lincs
continuation             = no
lincs_order              = 4
lincs_iter               = 1
lincs-warnangle          = 30
morse                    = no




Best Regards,

Daniel

-- 
Daniel Bauer, M.Sc.

TU Darmstadt
Computational Biology & Simulation
Schnittspahnstr. 2
64287 Darmstadt
bauer at cbs.tu-darmstadt.de

Don't trust atoms, they make up everything.