[gmx-developers] Re: Various integrator questions

Berk Hess hessb at mpip-mainz.mpg.de
Wed Aug 10 15:13:25 CEST 2005

> I think molecular scaling has the advantage that it doesn't interfere 
> with intramolecular constraints. The Kalibaeva et al. paper is one of 
> those with more equations than text, but I think it leads to a quite 
> usable result. The use of molecular virial doesn't seem to add 
> complexity with respect to the atomic virial. I haven't really 
> dissected all the details, but I see that they are using SHAKE. The 
> point is to call it at the right stage of the Trotter decomposition, 
> it seems.
> I'm convinced that the molecular virial is the way to go for, say, a 
> box of water. But in the case of a huge protein in the middle of a not 
> so huge box, I can imagine how it could pose some problems at the 
> boundary of the protein. If you think about a homotecy centered at the 
> middle of the box, the first water shell would move a lot with respect 
> to the protein surface, which is not scaled. I don't know about how 
> the compressibility of the proteins should look like. Maybe one could 
> think about a "residue virial" since we use constaints usually only 
> inside a residue. But this is science fiction, sorry.

My personal opinion is that assigning atoms to molecules in an artifical 
The atoms are the entities that exert on each other and what you would 
a molecule can differ depending on the circumstances. One can, for instance,
connect to molecules by a constraint for PMF calculations.
Also there are periodic systems, like I am simulating currently where a 
molecule is
connected periodically to itself in the z-direction (also with constraints).
Here it is impossible to use a molecular virial.

But a more pratical points is that the fast virial calculation algorithm 
is one of
the reasons why Gromacs is so fast.
Of course one would like to have everything exactly correct, but in some 
that results in algorithms with too limited use.

In this case I would argue that one could make the coupling time long enough
that the effect of the constraints becomes negligible.


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