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Re: [ESPResSo-users] PDB files

From: Peter Košovan
Subject: Re: [ESPResSo-users] PDB files
Date: Mon, 9 Nov 2015 14:55:12 +0100

Hi Paul,

The writing of PDB files is a workaround for writing generic particle configurations in a format originally designed for storing coordinates of atoms in proteins. PDB files contain a lot of entries that are not used by Espresso. As far as I have understood, "Fe" is used because iron can have an arbitrary number of bonds, so vmd does not complain if you have a branched structure. In general, vmd tries to guess a number of things from the atom type (its size, colour, number of possible bonds and their length...), so replacing type FE with another element might not lead to the result you desire.

If you want to write your particle coordinates in a format which more closely corresponds to how they are represented in Espresso, I recommend using the vtf/vsf/vcf file format.

Since vtf has been around, I personally consider the use of pdb in Espresso as obsolete. Only a fraction of their content stores information useful for Espresso. The rest is generic data which cannot be omitted because the format relies on a fixed number of characters on a line.



On Mon, Nov 9, 2015 at 2:27 PM, Paul Peterson <address@hidden> wrote:

I'm quite new to ESPResSo and MD simulations in general, so mine could be a very naive question. 

I have two types of particles and in my simulations. 
In output files produced by writepdb, all my particles are (arbitrarily) labeled "Fe", although the type distinction is preserved (last column). That's the reaon, I suppose, why Jmol will display them all the same, nor do I find a way to colour them according to the type. 

I looked for options in the writepdb command, but couldn't find any in the Manual.
Any suggestions (also about more conveniente file formats)?



Dr. Peter Košovan

Department of Physical and Macromolecular Chemistry
Faculty of Science, Charles University in Prague, Czech Republic

Katedra fyzikální a makromolekulární chemie
Přírodovědecká fakulta Univerzity Karlovy v Praze
Tel. +420221951290
Fax +420224919752

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