[gmx-users] GROMACS and XML

David van der Spoel spoel at xray.bmc.uu.se
Wed Apr 17 20:31:48 CEST 2002

On Wed, 17 Apr 2002, Anton Feenstra wrote:

>Just as a small note: I would suggest the possibility of *adding* QC
>information in stead of replacing the ff by QC. That opens the way to
>a QM/MM approach, similar to what Gerrit is already implementing.

You're right. My point was more general: one wants to be able to replace 
one force field by another, or maybe one basis set by another. So in 
practice this would mean the one has a force field and/or basis set.

The other thing for making this general is that the simulation parameter 
section can be replaced if you want to use this with another program.

>> 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.
>But it would also allow a quite rigorous error-checking, i.e. wheter
>all bonds defined in the topology actually are defined parameters in
>the forcefield description as well.
This is correct too, but first of all much of the check and algorithms are 
already implemented in pdb2gmx, and secondly XML can be used to enforce 
quite strict organisation of the data, which makes it easier to validate.
Obviously not everyone will want to touch the force field stuff, but when 
they do it is nice to enforce a structure (and give tools to validate).
Also, when I specify a residue like AIB which exist in the GROMACS force 
field files, but not in say AMBER, and I then switch to AMBER, there 
should be checks and clear messages about it. So the real consistency 
checks is still on the software side, although even there XML tools can 

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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