I am using prmed to load topology files and running simulations with
openMM. However, I want to change Lennard-Jones parameters for some atoms
(especially zero-radius hydrogens). In case of wild conformational search,
these zero-radius hydrogens cause nasty problems due to electrostatic
interactions.
Before create openMM's system, I guess I need to modify them by giving tiny
values to both epsilons and sigma.
This is the part of my python script.
prmtop = pmd.load_file('model.prmtop')
# something for changing lennard-jones parameters
system = prmtop.createSystem()
So far, I tried to modify atom.epsilon and atom.sigma in prmtop.atoms, but
it does not seem to work.
I know that I can use interactive parmed and modify the topology file. I
just want to know if there is a possible way in script-level without
modifying the topology file.
--
Best,
InSuk Joung
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Received on Fri Jan 08 2016 - 01:00:05 PST
