[gmx-users] Re2: problem wiht topology and gmxdump...

[Anton Feenstra]

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 [115]=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[115]' to be listed somewhere else in combination
with the relevant atoms.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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