[gmx-users] 6 degrees of freedom

Anton Feenstra feenstra at chem.vu.nl
Tue Jun 4 13:32:38 CEST 2002

jozef hritz wrote:
> How? E.g. I'd like to find eguilibrium distance between this protein and
> other structures. Do You think it's so easy to calculate? But in each case
> it has to be possible to simulate, hasn't it?

No, it is not easy if there is another 'structure', since that involves
the equilibrium for all possible interactions of your protein and the
'structure'. But in that case also 'freezing' all internal coordinates
for your protein will not give you much gain in simulation efficiency;
the hard work is still to calculate all interactions. Especially if you
use solvent; that accounts for >90% of the work! If you don't use
I would not trust the results, but you might have reasons to disagree on
that point. In that case, there might actually be something to gain, 
because freezing the internal freedom for the protein will allow you to
use a much larger timestep, since in effect only the whole protein
This is sometimes called 'rigid body dynamics' (for obvious reasons),
but unfortunately, there is no easy way to do this in Gromacs. The only
way I can think of right now, is to make an elaborate dummy-atom
construction. First, you put all the mass into three particles that
do not have interactions (no charge, no Van der Waals), and connect
these three together with constraints in such a way that they represent
a reasonable way the center of mass and moments of inertia of your
Then, you calculate dummy atom parameters for each of the original atoms
in your protein, that construct the atoms from your three mass
This is pretty tedious work, since the parameters must be just right to
get all atoms in the proper position with sufficient accuracy. Choosing
the orientation and distances of the mass particles in a smart way (i.e.
in a orthogonal frame) can make this a little bit easier.

This construction will be similar (though infinetly more complex) to 
that I devised for aromatic sidechains, as described in the .pdf manual
on page 112 (section 'Out-of-plane vibrations in aromatic groups').

I'm sorry if this is not particularly helpful, but it's the best I can
think of.


 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
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|  \__/  | "I Calculate My Birthright" (P.J. Harvey)                 |

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