[gmx-developers] Re: Various integrator questions

Michel Cuendet michel.cuendet at epfl.ch
Wed Aug 10 17:56:37 CEST 2005

Hi Berk,

Berk Hess wrote:

> My personal opinion is that assigning atoms to molecules in an 
> artifical distinction.
> The atoms are the entities that exert on each other and what you would 
> consider
> a molecule can differ depending on the circumstances. 

In general, a lot of the compressibility is due to nonbonded interaction 
between solvent molecules. That's the motivation for molecular scaling.

> 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. 

I agree on all that. It seems that the atomic scaling is then  more 
general. Also in the case of membranes or DNA, molecular scaling doesn't 
make sense. In particular, I think molecular scaling (like in Kalibaeva 
et al.) is justified only with many small molecules. It can be 
problematic with big molecules. I don't know if it possible to do use 
molecular virial to estimate the pressure, and then scale the atoms 

> But a more pratical points is that the fast virial calculation 
> algorithm is one of
> the reasons why Gromacs is so fast. 

The molecualar virial is also fast, because all (large) intramolecular 
forces cancel out and don't have to be taken ino account. A lot of noise 
is avoided like this.

> Of course one would like to have everything exactly correct, but in 
> some cases
> that results in algorithms with too limited use. 

I never really said molecular viriral is "more correct" than the atomic 
one. The implementation of the atomic scaling with constraints might 
just be more tricky. You can also write correct RESPA-like integrators 
for the atomic case. This paper seems very interesting:

M. Marchi, P. Procacci
/Coordinates Scaling and Multiple Time Step Algorithms for Simulation of 
Solvated proteins in the NPT ensemble/
J. Chem. Phys., 109, 5194 (1998)

Ciccotti et al. J. Phys Chem B, 105, 6710.

There is also a nice review in which they give a Trotter decomposition 
of an atomic scaling scheme (without constraints).

P. Procacci, M. Marchi
/Multiple Time Steps Algorithms for the Atomistic Simulations of complex 
molecular systems/
Proceedings of the NATO-ASI School, Erice 11-21 June 1998
/ Advances in the Computer Simulations of Liquid Crystals /
C. Zannoni and P. Pasini Editors, 333-387, Kluwer Academic publishers, 
Dodrecht the Netherlands (1999)

Of course, the best would be that the user can choose which pressure 
scaling she wants...



Michel Cuendet, Ph.D. student
Laboratory of Computational Biochemistry and Chemistry
Swiss Federal Institute of Technology in Lausanne (EPFL)
CH-1015 Lausanne						
Switzerland                            Phone : +41 21 693 0324
lcbcpc21.epfl.ch/~mitch	                       +41  1 633 4194

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