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

[Andreas Mecklenfeld]

Hello Mark,

thanks for the reply. The point is, I don't. I found some Lennard-Jones 
parametrization in literature that distinguishes between intra- and 
intermolecular (oxygen atom of water) 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.

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
>>
>> --
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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