[gmx-users] Water molecule starting at atom 18511 can not be settled
chris.neale at alum.utoronto.ca
Sat Apr 16 19:17:26 CEST 2016
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
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.
On Sat, Apr 16, 2016 at 5:01 PM, Mark Abraham <mark.j.abraham at gmail.com>
> 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
> 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
> > 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
> > in mailing list but no helpful solution has been proposed yet.
> > So any solution would be highly appreciated.
> > Cheers,
> > Alex
> > --
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