[gmx-users] Problem with topology and gmxdump....

[Anton Feenstra]

sgaray at fbcb.unl.edu.ar wrote:

> Hi all
[...]
> The problem is that gmxdump don´t give me the LJ parameters that will be 
> used the program for the calculation, because just only give me the LJ 
> parameter for atoms and not for the [nonbond_params] that I set for some 
> pairs of atoms.

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.

> Why if I´m using the same files for my two systems can´t obtain the same 
> LJ parameters?
> The unique differences are the mdp file, the gro file and the top file 
> which include in one case the information about stearic acid alone and 
> the other case the stearic plus the probe.
> 
> How can I know the LJ parameters that gromacs is realy using?

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.


-- 
Groetjes,

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