[gmx-users] Re2: problem wiht topology and gmxdump...
feenstra at chem.vu.nl
Fri Jan 23 10:59:10 CET 2004
sgaray at fbcb.unl.edu.ar wrote:
> Dear Dr. Feenstra, I have some other questions about your answers:
>>IIRC, you can only have one global [nonbond_params] directive.
>>So, if you have one in each of your .itp files, I think it won't work.
> I have only one file with the [nonbond_params].
>>These are in the .tpr file, as you saw using gmxdump. I'm not sure
>>exactly how they are organized, but in general there should be
>>'general' parameters for different atom types, and then some
>>specific parameters for some pairs of atom types. gmxdump may
>>list all pairs of atom types explicitly.
> I´ve been seen the gmxdump outfile in detail. I have 11 atomtypes
> defined. I found 121 LJ functypes (how can calculate this quantity:
> 121. Is that all posible variations,n^2? ). The file just only shows all
> pairs of LJ14 interactions but not the pairs of LJ interactions. Is it
> wrong?. I understand that in the topology file shouldn´t appear all LJ
> interactions (atom by atom) because that depend the position of the
> particles, but I would like to know wich LJ interaction is used by
> gromacs between each pair of atomtypes. The LJ functypes which
> are described by the gmxdump_outfile don´t say anything about
> which atoms are involved. Example:
> functype =LJ C6 2.52514891e-03 C12 2.11139763e-06
> I don´t know which atomtypes are involved in that interaction.
> Could you tell me how gromacs build my 121 LJ functypes ?
I'm not sure how it is exactly with LJ, but in generatl, the topology
is arranged in function types, defining the parameters as you show
above, and atoms for which a certain function type applies. So, in your
case I'd expect 'functype' to be listed somewhere else in combination
with the relevant atoms.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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