Re: [h5md-user] tentative of synthesis: parameters, box size, particle number

[Konrad Hinsen]

On 14 sept. 11, at 09:39, Pierre de Buyl wrote:

> 2. box size
>    - The offset should be given, each in their "H5MD containter"  
> with step and time.
>    - How different is what we do with respect to, for instance, PDB  
> or gromacs ?
>       see the manual of gromacs, chapter 3, §3.1 and §3.2 at http://www.gromacs.org/ 
>  second news item or direct link ftp://ftp.gromacs.org/pub/manual/manual-4.5.4.pdf
>      pdb http://www.wwpdb.org/documentation/format33/sect8.html

I don't know about Gromacs, but all about PDB. It's a format for  
storing crystal conformations, so they follow crystallography  
conventions. It's also a format for single conformations, so time  
dependence is not an issue.

The size of the unit cell is given by the three edge lengths (a, b, c,  
in Angstrom), and the shape by three angles (alpha, beta, gamma, in  
degrees). The first lattice vector points along the x axis, the second  
lies in the x-y plane. Symmetry is specified by the name of the  
symmetry group, which implies a set of symmetry transformations and  
constraints on the unit cell shape, but those are supposed to be known  
(tabulated), so they are not stored explicitly.

The PDB conventions are not very practical for simulations. Simulation  
programs need the lattice vectors, not their lenghts and angles. The  
use of named symmetry groups isn't practical either, unless we want  
all simulation programs to incorporate the tables published by the  
IUCr (International Union of Crystallographers).

>    - I am not in favour of storing in fractional coordinates, for my  
> data at least. How would that work ?

It's possible, not but practical. I don't see any advantage.  
Fractional coordinates are good for symmetry operations because that  
makes them time independent in all practically relevant situations.  
Most MD simulations don't need symmetry operations anyway.

>    - If I understood correctly, the latest suggestion is to store,  
> for each time frame, a set of transformations and a shift ?

No, only once for the whole trajectory.

> Thanks for your various suggestions, and sorry if it looks like I'm  
> not understanding everything. I am not familiar myself with non- 
> cubic boxes, understand that they are very useful in many  
> situations, and at the same time would like to keep "H5MD 0.1"  
> simple enough.

Non-cubic is a must for macromolecules. Cuboid is the minimal  
requirement, but many simulations also need non-orthogonal boxes.

Konrad.
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research at  khinsen dot fastmail dot net
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