[gmx-users] Freeze groups and rotation

Allen Smith easmith at beatrice.rutgers.edu
Thu Aug 16 06:59:47 CEST 2007

Freezing fixes atoms in place in at least 1 dimension. If one fixes atoms in
place in all 3 dimensions, can they still rotate? In particular, if one
fixes the oxygen atoms of water in place, can the hydrogens still rotate?
And how does making hydrogens into virtual sites affect this? Is the case
different for fixing atoms in 2 dimensions or 1 dimension? I am
considering putting several layers of water around a protein (for homology
modeling) with the outermost layer(s) being frozen in position, but would
prefer to allow said layer(s) to rotate if necessary (e.g., to optimize
h-bonding), at least for layers other than the _very_ outermost one.



Allen Smith                       http://cesario.rutgers.edu/easmith/
February 1, 2003                               Space Shuttle Columbia
Ad Astra Per Aspera                     To The Stars Through Asperity

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