[gmx-users] degree of freedom

Mark Abraham Mark.Abraham at anu.edu.au
Thu Mar 1 02:45:41 CET 2007

Nicolas SAPAY wrote:
> Actually, I had a doubt on what happens when movements of the center of
> mass are removed and when the position of a molecule is constraint... Just
> wanted to check my calculations...

As a suggestion, if you say what your real problem is in your original 
question, you stand a much better chance of getting the answer you 
wanted, and a lower chance of irritating people who either think you're 
asking a trivial question or are wasting their time. The same goes for 
the CHARMM hydrogens thread :-)

Removing the solute COM motion degrees sounds like 3 or 6, which won't 
be significant. Frozen molecules don't have any DOF, but 
position-restrained ones will have a few (but nothing like 3N-5).


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