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

[Daniel Bauer]

Hi,

thanks for the response! Now i know what I have to do :)

So did I understand you right that the ion parameters that are currently
used in amber99sb by GROMACS are not identical with the ones implemented
in the current version of amber99sb used by AMBER? If yes, whats the
reason for this (might be more of a question for Justin or Mark). Are
there any plans to change this in future releases?


Best regards,

Daniel


On 05/08/2018 04:18 PM, Felipe Merino wrote:
> 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
>>
>

-- 
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.