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

jennifer johnston jen.johnston at lycos.com
Thu Oct 22 16:27:25 CEST 2009

An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091022/e9e4ae82/attachment.html>
-------------- next part --------------

 >1. Re: COM removal type angular with PBC? (Mark Abraham)

>> Dear All,

>> I'm attempting to simulate a dimeric protein in an explicit 

>> bilayer/water environment. I'd like to remove the translation &amp; 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?

Thanks very much indeed for your response, Mark.
I'm using Metadynamics (Laio &amp; Parinello), with some carefully selected collective  variables to investigate the nature of the interface between the two protomers. The reason for trying to reduce the translational and rotational degrees of freedom for one of the protomers is to try to obtain convergence on my deliberately limited free energy surface.

Basically I just want to know if what I've tried, here below, is not going to work for reasons other than perhaps I implemented it wrongly, i.e. because it was never intended to work on an explicit system with PBC and 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?

>No there's no implementation of that.

Thanks for letting me know!


More information about the gromacs.org_gmx-users mailing list