[gmx-users] SR and LJ energies

[Anton Feenstra]

Michal Kolinski wrote:

> Hi all.
> 
>  
> 
> I'm simulating receptor in membrane with ligand (morphine) inside the active site of the protein.  Topology for ligand I obtained using PRODRG  server (I checked it, and the topology seems OK).  My question is about LJ and Coulomb (ligand-receptor interaction) energies I got for my 1ns MD.  I wonder why all coulomb energies are so low?  Is it normal in gromacs? 
[...]

Not sure if this is the same problem, but I helped out one of our 
students yesterday who wanted to run one of the Gromos ff's with 
reaction field (as one should). Problem was, he'd set epsilon_r to 62, 
but kept coulombtype = cut-off. The result is, you scale down charge 
interactions by a factor of 62, and you don't use reaction field. FOr 
that, you'd have to set coulombtype = reaction-field.

This can be (in fact, has been) very confusing! Also, there is no way in 
the current implementation to use reaction field *and* scale charge 
interactions. So, I'd say there actually should be a separate parameter, 
eps_reaction_field or some such, to set the reaction field.


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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