jennifer johnston wrote:
Dear All,
I'm attempting to simulate a dimeric protein in an explicit
bilayer/water environment. I'd like to remove the translation & rotation
of one protomer relative to the other, so that one protomer is able to
move around relative to the stationary one. I'm using semiisotropic
pressure coupling.
That's not yet a well-formed strategy. What motions are to be permitted
relative to the bilayer?
I looked at using COMM_MODE = angular, with the comm group being the
backbone of the stationary protomer. (This is because I'd prefer not to
apply posres to individual backbone atoms, if possible...)
I ran the simulation, adn it seems that the stationary protomer is not
really anymore stationary than the free one.
When I look at the posts relating to the use of angular com motion
removal, most of the discussion seems to suggest that it is not
advisable to use angular com motion removal with PBC, and not really
advisable to use it for a small part of a system, as I've tried to do..
but much of the discussion relates to vacuum simulations. Do I conclude
correctly, that what I've tried just categorically will not work for an
explicit system??
Finally - if I am correct - then is there a different way of applying a
position restraint to the com of a group - rather than to explicit atoms?
No there's no implementation of that.
Mark
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