[gmx-users] energy monitoring

David spoel at xray.bmc.uu.se
Fri Nov 22 18:33:09 CET 2002

On Thu, 2002-11-21 at 19:09, Ghermes Chilov wrote:
> Hello!
> We've faced some problems concerning energy file (.edr) processing:
> A. when trying to extarct energy components with g_enemat, the program
> returns that it can't find some terms (like LJ-LR: SOL-SOL) in the
> file, however LJ: SOL-SOL is present (and this is more than enough for
> our purposes). Segmentation error is returned and the program quits.
> __ How to quit LJ-LR calculations when we don't need them?
This is non-zeo only when you have twin range cut-off.

> B: Are there any limitations on the string size in the .mdp file?
> Namely, if we have a lot of energygroups (say 200 aminoacids and 1
> ligand) and we wish to skip dynamics of the first 200 groups by
> freezing them, how can we add 200x200 entries into string
> 'freezegrps'? I mean, can the program accept such a long string?
No. You will have to modify gmx/src/kernel/readir.c 
You can not have more than 256 groups, unless you modify the type that
holds the groups (in atoms and mdatoms structures)

> Thanks for attention!
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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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