[gmx-users] calculate number of contacts

[Attilio Vargiu]

Hi All
I want to calculate the number of contacts between a small molecule and a
oligonucleotide from a MD run.
I read in the manual that in the itp file is possible, setting 2 for the
combination rule within the section [ defaults ], to give sigma and
epsilon instead of c6 and c12 LJ parameters.
If I'm not wrong, the value of the interaction at the equilibrium point is
-epsilon, so putting epsilon=1 for all but hydrogens atoms types in itp
file, and setting a cutoff of 3.5 or 4 angstrom, re-running the trajectory
with the proper groups in energy specifications, I should approximately
get the number of contacts.
Unfortunately this seems not to be the case, I get a number of contacts of
one order of magnitude bigger than expected, but I do not understand
what's going wrong...

There is something I'm missing or misunderstanding?
Can anyone help me?!?!?!?

Thanks in advance
Attilio

---------------
Attilio Vittorio Vargiu
PhD in Biophysics at SISSA/ISAS
via Beirut 2-4, Trieste (Italy)
phone: 00390403787335

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