[gmx-users] Water molecule starting at atom 18511 can not be settled

[Alexander Alexander]

Dear Christopher,

If it is not a default, I have not applied any "SETTLE" in my calculation
as far as I know. Here is the .mdp file of my minimisation. Also the
"define = -DFLEXIBLE" did not help.

-----------------------------------
define = -DFLEXIBLE
integrator = steep
;integrator = cg
;integrator = l-bfgs
emtol = 10
emstep = 0.0001
nsteps = 100000000
nstlog = 1
nstenergy = 1
nstlist = 10
ns_type = grid
coulombtype = PME
rcoulomb = 1.26
vdwtype = cutoff
rvdw = 1.26
pme_order = 4
optimize_fft = yes
;constraints = all-bonds
;constraint_algorithm = LINCS
cutoff-scheme = Verlet
;rlist = Cut-off distance for the short-range neighbor list.
pbc = xyz
------------------------
Cheers,
Alex


On Sat, Apr 16, 2016 at 7:02 PM, Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> Then don't use settle for your minimization?
> (mdp option define = -DFLEXIBLE for most water models)
>
> You can always turn it on again and run another EM after whatever
> problematic configurational feature has relaxed.
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Alexander
> Alexander <alexanderwien2k at gmail.com>
> Sent: 16 April 2016 11:57
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Water molecule starting at atom 18511 can not be
>      settled
>
> Dear Mark,
>
> Thanks for your response.
> If I understood your statement correctly, I would say these numbers used
> here for the epsilon and sigma are not arbitrary but they come from some
> well quantum calculations (DFT) of water on this surface, actually,
> adsorption energy and optimized geometry of water on the surface were used
> in Lennard-Jones potentials to get sigma and epsilon, this means it is a
> sound model physics.
>
> Cheers,
>
> Alex
>
>
> On Sat, Apr 16, 2016 at 5:01 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > You will always need a sound model physics and a starting configuration
> > that is close enough to consistent with that. Which aspect do you think
> is
> > wrong?
> >
> > Mark
> >
> > On Sat, Apr 16, 2016 at 3:58 PM Alexander Alexander <
> > alexanderwien2k at gmail.com> wrote:
> >
> > > Dear Gromacs user,
> > >
> > > The minimisation (steepest descent) of water on surfaces of a nickel
> > > intermetallic compounds works fine if epsilon in the nonbond_params
> below
> > > is 17.0 (harvested from LJ(10-4)) but it will crash immediately if
> > epsilon
> > > is elevated to 64.65 (harvested from LJ(12-6) or LJ(9-6)) with settling
> > > problem of one water molecule.
> > >
> > > [ nonbond_params ]
> > > ;     ai       aj    funct     sigma(nm)      epsilon (kj/mol)
> > >       Ni     OW     1          0.2072             64.65
> > >
> > > The settling problem of the molecule has been already discussed many
> > times
> > > in mailing list but no helpful solution has been proposed yet.
> > > So any solution would be highly appreciated.
> > >
> > > Cheers,
> > > Alex
> > > --
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