[gmx-users] KCl forms crystals at c=0.15M with amber99sb-ildn
Mark Abraham
mark.j.abraham at gmail.com
Fri May 11 15:19:20 CEST 2018
Hi,
On Fri, May 11, 2018 at 12:07 PM Daniel Bauer <bauer at cbs.tu-darmstadt.de>
wrote:
> 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?
Please everybody be very careful with statements like this. Generally the
definition of a force field should never change, so that results remain
reproducible. This is why derivatives of forcefields have been made, while
correcting some observed deficiencies. However, since e.g. the original
validation of the AMBER ports within GROMACS were made against AMBER 8,
there have been some corrections of typos, etc. made by AMBER developers,
which AFAIK have all made their way to the GROMACS files.
> 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?
>
First let's clarify whether anything really had its definition changed ;-)
If there's a recognized variant, then e.g. someone might contribute it to
http://www.gromacs.org/Downloads/User_contributions/Force_fields so that
people using it understand that it's a case of "buyer beware." These days
we feel it would not be appropriate to add support for a new force field in
GROMACS (say, CHARMM36) unless that change came alongside scripts that
would be able to verify that the implementation remains correct, even
though both GROMACS and the software for which it was developed will have
to change as time passes. (So that issues like
https://redmine.gromacs.org/issues/2046 are found and prevented early.)
Mark
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
> <https://maps.google.com/?q=cs_order%C2%A0%C2%A0%C2%A0%C2%A0%C2%A0%C2%A0%C2%A0%C2%A0%C2%A0%C2%A0%C2%A0%C2%A0%C2%A0&entry=gmail&source=g>
> = 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.
>
> --
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