[gmx-developers] XML files

David van der Spoel spoel at xray.bmc.uu.se
Thu Mar 21 23:42:25 CET 2002

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 
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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