[gmx-developers] XML files

[David van der Spoel]

On Thu, 21 Mar 2002, Erik Lindahl wrote:

>Actually, it would be nice to have units on all output and step stuff, 
>so you could say that you want
>100 ps of simulation with 2 fs timestep, and energy file output every 10 
>ps. I don't think it affects the DTD, though, so we can do that later.
>
>Is it possible to include help texts with a longer description of each item?
That would solve it immediately. I'll look into it...


>Agreed; but it would be darn nice to have! By the way, since you've been 
>doing NMR stuff - I think it would be nice to be able to use atom names 
>instead of numbers when describing bonds, etc. What's the most common 
>way people would be adding NMR or X-ray restraints, and how do they 
>select their atoms?
It will be labels anyway, rather then numbers. But that would be something 
like:
SER67 OG - SER67 HG
Of course that get's really out of hand as a way to store a complete 
protein topology. Esepcially when you have multiple SER67 (chain id's)

An alternative would be to always generate bonds angles and dihedrals 
rather than list them... A bit tedious maybe.

>>We'll keep trr and xtc obviously for space reasons, maybe we need to keep 
>>gro for a while...
>>
>And some kind of file format that doesn't use RPC libraries..  Even if I 
>rip the RPC stuff from linux we can't be sure it will work 'everywhere'. 
>I don't have the slightest idea what will happen with 64-bit windows, 
>for instance...
Actually I looked into this long ago. It's not trivial, you're basically 
porting system libraries. No joy...

-- 
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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