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

[Felipe Merino]

Hi,

I think the problem comes from the ion parameters within the "vanilla" 
amber forcefieCld. If I'm not mistaken, the parameters in the gromacs 
port are the Aqvist parameters, which are known to make this little 
trick. In the past, we have used the Smith/Dang parameters for 
simulations nucleic acids (Dang LX (1995)  J Am Chem Soc 117: 6954–6960) 
although I think amber is using now Tom Cheatham's parameters (J. Phys. 
Chem. B, 2008, 112 (30), pp 9020–9041).

I hope that helps
Best
Felipe

On 08/05/18 15:54, Daniel Bauer wrote:
> 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
>

-- 
Felipe Merino,
Max Planck Institute for Molecular Physiology
Department of Structural Biochemistry
Otto-Hahn-Str. 11
44227 Dortmund
Phone: +49 231 133 2307

ORCID:  https://orcid.org/0000-0003-4166-8747
Publons: https://publons.com/a/1305699/
Researchgate: https://www.researchgate.net/profile/Felipe_Merino