[gmx-users] GROMACS and XML

David van der Spoel spoel at xray.bmc.uu.se
Wed Apr 17 19:40:55 CEST 2002

On Wed, 17 Apr 2002, Peter Murray-Rust wrote:

>One general rule: for every XML element ("tag") you create software has to 
>exist! So always bear in mind how the XML is to be processed. For CML we 
>have three approaches - XSLT (probably the easiest and most generally 
>applicable), CML-DOM and CML-SAX. I expect that in computational chemistry 
>the XSLT approach will initially the most useful.
>I certainly don't want to reinvent anything that has already been done - is 
>the GROMACS DTD reachable from the website or is it in a CVS repository?

THere is some stuff in the relaese (share/top/gromacs.dtd) but it's still 
under devlopement. You will find newer versions in the CVS. I think I have 
the description of macromolecules solved at a level that we can describe 
generally the construction of a macromolecule from building blocks (e.g. 
amino acids) and the links between them (including peptide links, cys-cys 
bridges etc.). Furthermore we have added  elements to the DTD for 
describing modifications to amino acids, e.g. N- and C-terminus, but also
other modifications, e.g. methylation of a Lysine chain can be described 
this way. The big point I want to put through is separation of molecule 
description from force field description. Basically the GROMACS input 
should consist of three parts:
1. Molecule description
2. Force field description
3. Simulation parameters

My current way of thinking is to create 3 DTDs which then are combined 
into one master DTD. One could also conceive having quantum chemical 
information instead of 2 (i.e. basis sets). 

A practical  drawback of separating 1 and 2 is that a certain amount of 
information has to be duplicated. E.g. in 1 we would specify that there is 
a bond between N and Ca in an Ala residue, this information would also 
have to be incorporated in 2 in some way, to be able to add the 
appropriate bond length and force constants.

Sorry for the long expose, but it would really be beneficial to cooperate 
with you, since you have much more experience in XML. One reason we didn't 
base our efforts on CML is exactly the lack of macromolecule support, but 
also I found the use of schema rather (maybe even overly) complicated.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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