[gmx-users] COM removal type angular with PBC?

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 22 00:31:00 CEST 2009

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.


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