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

From: Konrad Hinsen
Subject: Re: [h5md-user] tentative of synthesis: parameters, box size, particle number
Date: Thu, 15 Sep 2011 21:28:29 +0200

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 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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