[gmx-users] SR and LJ energies
feenstra at few.vu.nl
Fri Jun 17 11:01:11 CEST 2005
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.
* NOTE: New Phone & Fax numbers (below) *
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610 |
| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" (RHCP) |
More information about the gromacs.org_gmx-users