[chimera-dev] Material science feature requests

[Thomas Goddard]

Here is email I exchanged with Chris Greenwell about using Chimera
for a material science / molecular dynamics study.

    Tom

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Date: Thu, 21 Oct 2004 09:14:55 +0100
Subject: Re: Material visualization with Chimera
From: "H. Chris Greenwell" <h.greenwell at ucl.ac.uk>
To: Thomas Goddard <goddard at cgl.ucsf.edu>

Hi Tom,

First of all, Chimera is fantastic!  Congratulations!

Yes, I noticed the problem with large numbers of atoms.  We run systems 
getting on for 500,000 atoms., but most are less than 100,000 atoms.

I still use the Atom Eye software, which is more efficient at using 
memory (http://164.107.79.177/Archive/Graphics/A/) for large models.  
However, it is less intuitive to use and doesn't have much of the 
functionality that we would like.

The type of work we do at the moment involves simulating the interlayer 
region of layered clay type structures with organic molecules, such as 
long monomers, between the crystalline clay sheets.  We do this to gain 
insight into the interlayer arrangement and dynamics not attainable by 
experimental means.  We have to present data which is both meaningful 
and interesting to the experimental community.

We use the LAMMPS code as our large-scale MD engine, from Sandia.  We 
have our own data analysis tools to generate RDFs, diffusion 
coefficients and atom density plots.  However, in order to make sense 
of the features, and to spot unusual features that get averaged in the 
data of these numerical data sets it is necessary to visualize the 
model through the simulation.  As an ex-experimental chemist I have a 
strong bias to the visual!

I have looked at many types of software, and essentially we have two 
considerations:

1) A visualizer for looking at each frame, and movies of the atom 
positions.  Data analysis as described above.

2) A builder for loading crystalline unit cells, generating organic 
monomers, translating, rotating and deleting atoms/molecules.  
Critically, we tend to use periodic boundary conditions in all our 
simulation so an ability to replicate unit cells and visualize the 
boundary markers when desired.  Functionality to place forcefield atom 
types on the system is also needed.

I have come across only two contenders to do this with:

ECCE (http://ecce.emsl.pnl.gov/) looks promising and is free to 
academia, however, as with many freeware builders/visualizers, it is 
only for bio-systems and has no concept of periodic unit cells.  I also 
am unaware of the atom number capability.

Materials Studio/Cerius 2.  These are the commercial options from 
Accelrys and work very well.  Unfortunately, these are also incapable 
of building models greater then approx. 30,000 atoms for materials 
science.  Materials Studio has a bug, which stops it doing this, and 
Cerius 2 (a) gets very slow, and (b) has a purely numeric atom 
numbering, which has a 5 digit capacity and relies on the molecules 
being made up of residues.

We are starting to use the latest LAMMPS2003 software from Sandia, and 
may well look at steering it in the future, so any developments in 
Chimera to aid us in looking at materials would be much appreciated.

Many thanks

Chris

On Thursday, October 21, 2004, at 12:02 AM, Thomas Goddard wrote:

> Hi Chris,
>
>   Dave Konerding told me you tried using Chimera to visualize materials
> with large numbers of atoms.  Unfortunately Chimera uses alot of memory
> per atom (~2 Kbytes) and gets pretty slow for systems of 100,000 atoms
> or more.
>
>   I'm curious about what you are looking for with Chimera and whether
> there are new features you would need.  We primarily focus on proteins
> and nucleic acids but would consider adding features to help in 
> materials
> science.
>
>       Tom Goddard
>       Chimera developer
>       UC San Francisco
>
>
H. C. Greenwell
EPSRC Fellow
Centre for Computational Science
Christopher Ingold Laboratories
University College London
20 Gordon Street
London WC1H 0AJ
United Kingdom


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Date: Thu, 21 Oct 2004 10:54:31 +0100
Subject: Chimera materials visualization wish list
From: "H. Chris Greenwell" <h.greenwell at ucl.ac.uk>
To: Thomas Goddard <goddard at cgl.ucsf.edu>

Hi Tom,

I realise that in my earlier e-mail I have only outlined general 
points, and therefore have only addressed part of your email.

Therefore, if I could compile an initial wish-list of new features 
(apologies if some of this is already in the code, as I am still 
getting to know it) it might look something like:

1)  To be able to import the common file types we use in our 
simulations.  These are: (a) the LAMMPS 2001 output files (.pos), which 
are largely XYZ files with a time step and an atom type number related 
to, (b) the LAMMPS 2001 data file (.dat/.lmp), which contains the atom 
information (masses), coordinates and bonding. (c) the LAMMPS 2003 
data/position files, which I think are a little different but will be 
used by us in the near future.  (d) the Accelrys Biosym coordinate 
(.car) file, topology (.mdf) file and trajectory (.arc/.trj) files.  
Dave kindly put together a little utility for the .car/.mdf file.

2) To be able to remap any atoms that have moved outside the cell, 
within the cell boundaries when visualized.

3) To be able to view the cell boundaries as a dashed/solid/no line.

4) To be able to replicate the viewed model in XYZ directions so that 
motion across cell boundaries can be followed.

5) To be able to turn the replicated unitcells into one supercell (we 
have an utility to do this with .car/.mdf) .

6) To be able to display and select atoms on the basis of forcefield 
atom types.

7) To be able to render crystalline structures as polyhedra.

8) After visualizing, or performing molecule/atom 
translations/deletions/insertions etc, to be able to export as the file 
types listed in (1) and also the Atom Eye (.cfg) format.

Many thanks

Chris

H. C. Greenwell
EPSRC Fellow
Centre for Computational Science
Christopher Ingold Laboratories
University College London
20 Gordon Street
London WC1H 0AJ
United Kingdom