[gmx-users] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

[Mark Abraham]

Hi,

On Fri, Aug 12, 2016 at 9:16 AM Andreas Mecklenfeld <
a.mecklenfeld at tu-braunschweig.de> wrote:

> Hello Mark,
>
> thanks for the reply. The point is, I don't.


Ah, I read your original email more closely now. The use of a subject line
that reflected your error message rather than your intention confused me.


> I found some Lennard-Jones
> parametrization in literature that distinguishes between intra- and
> intermolecular (oxygen atom of water) interactions.


Um, typical water models have no intra-molecular LJ interactions.


> My intention was
> thus to define the specific eps_ij and sigma_ij for the corresponding
> atomtypes, which I thought should be dealt with in the [ nonbond_params
> ] section. All parameters are for Lennard-Jones and this is the
> potential I want to use. I have no idea why the usage of Buckingham is
> assumed. I'm using Gromacs 5.1 btw.
>

Then somewhere (e.g. [nonbond_params]) you are using a number that is being
interpreted as a function type that is Buckingham, which of course makes no
sense for a code that assumes each atom type has at most one set of LJ
parameters. But we haven't seen your full topology or full error message.

Mark


> Thanks,
> Andreas
>
>
>
> Am 11.08.2016 um 17:59 schrieb Mark Abraham:
> > Hi,
> >
> > How do you want your atoms with lj parameters to interact with atoms with
> > Buckingham parameters?
> >
> > Mark
> >
> > On Fri, 5 Aug 2016 08:53 Andreas Mecklenfeld <
> > a.mecklenfeld at tu-braunschweig.de> wrote:
> >
> >> Dear Gromacs-users,
> >>
> >> I'm trying to modify some intermolecular Lennard-Jones interactions
> >> based on the GAFF force field. I've altered the topology file according
> to
> >>
> >>
> >>
> ############################################################################
> >>
> >> [ defaults ]
> >> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> >> 1               2               yes             0.5     0.8333
> >>
> >> [ atomtypes ]
> >> ...
> >>
> >> [ nonbond_params ]
> >> type1    type2    sigma    epsilon
> >> ...
> >>
> >> #include ...
> >>
> >>    [ system ]
> >> ...
> >>
> >>    [ molecules ]
> >> ...
> >>
> >>
> >>
> >>
> >>
> ############################################################################
> >>
> >> Sigma and epsilon for atoms type1 and type2 are calculated according to
> >> the Lorentz-Berthelot combination rule. The error I receive is
> >>
> >> "Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)",
> >> though I obviously want to use LJ and did not intentionally set any flag
> >> for Buckingham. Is there any way to fix this?
> >>
> >> Cheers,
> >>
> >> Andreas
> >>
> >>
> >> --
> >> M. Sc. Andreas Mecklenfeld
> >> Stipendiat
> >>
> >> Technische Universität Braunschweig
> >> Institut für Thermodynamik
> >> Hans-Sommer-Straße 5
> >> 38106 Braunschweig
> >> Deutschland / Germany
> >>
> >> Tel: +49 (0)531 391-2634
> >> Fax: +49 (0)531 391-7814
> >>
> >> http://www.ift-bs.de
> >>
> >> --
> >> Gromacs Users mailing list
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> --
> M. Sc. Andreas Mecklenfeld
> Stipendiat
>
> Technische Universität Braunschweig
> Institut für Thermodynamik
> Hans-Sommer-Straße 5
> 38106 Braunschweig
> Deutschland / Germany
>
> Tel: +49 (0)531 391-2634
> Fax: +49 (0)531 391-7814
>
> http://www.ift-bs.de
>
> --
> Gromacs Users mailing list
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