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.
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?
Many thanks in advance for your help,
Jennifer
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