On 8/11/2011 8:24 AM, Anushree Tripathi wrote:
I want to simulate membrane protein in vaccum so let me know which
force field i can use for it.
Probably none of them - they were all parametrized on condensed-phase
data. In order to do such a simulation, you are going to have to
establish a valid protocol for so doing, and that means finding similar
work in the literature. So you will need to go and find such work. That
will begin to address the issue of force field choice.
Also I m doing simulation for the same protein in liquid using OPLS
force field.Please tell me is it correct?
OPLS has some demonstrated value for condensed-phase simulations.
Whether it is a valid or best choice for your context depends on a great
many things that you haven't mentioned yet, and that we wouldn't have
time to address if you had :-) Reading about what other people with more
experience than you have done is a necessary learning process.
Mark
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