Re: [AMBER] Freeze Atoms in Nab

From: David A Case <>
Date: Fri, 9 Dec 2016 21:17:27 -0500

On Fri, Dec 09, 2016, The Cromicus Productions wrote:
> I'm trying to perform NMA with some atoms frozen but I seem to keep
> walking into errors. Let's say I want to freeze the atoms 1-30,287-349,

Using the "frozen" atom mask won't do what you want it to: it artificially
zeroes out the forces on the affected atoms: it is for this reason that they
won't move during minimization or dynamics. I'm not sure what is done with
second derivatives.

Note that having frozen atoms violates Newton's third law, since interactions
between frozen and un-frozen particles end up with a force on the moving atom
but not on the frozen atom.

For dynamical simulations (like MD or normal modes), a consistent approach is
to edit the prmtop file to make the masses very large for the atoms you wish
to keep fixed.


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Received on Fri Dec 09 2016 - 18:30:03 PST
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