[gmx-users] RE:g_cluster crashes on large structures?

[K.A. Feenstra]

Mikko Huhtala wrote:
> 
> Sorry to reply to my own message. I realized that the problem was that
> I was trying to select the whole system for output. g_cluster works on
> the trajectory, if solvent is not output. So I guess the short answer
> is that I should be in the market fr more memory (and g_cluster is not
> a particularly memory efficient program?).

Right ;-) Inevitably, if you want to cluster conformations in a
trajectory, you need access to each and all of the frames. This
means that you will want to read all of them into memory. So,
the out-of-memory you encountered was not for the 55095*4 bytes
mentioned in the error message, but this was already the n-th time 
this was done for n frames in the trajectory (where n would be
approx 1G/(55095*4)...).

Of course, in this particular case were you cluster on C-a coordinates,
but you want output for the whole system it would be possible to
re-write the program to only use memory for the C-a coordinates
during clustering and re-read the whole trajectory for output only,
but I don't feel this is a general case.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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