Hi,
I've been trying to think of what could possibly be causing these
really long times, but I'm really not sure what is happening.
Unfortunately there just was not enough information in the post to
decipher the key to this problem. Is there something special about
those 7 residues? How accurate do you think their orientations are in
the PDB file you are using? And how accurate is the PDB file itself
with respect to all parts of the system?
Have you had a chance to investigate further as to what the issue
might be? For example, which part of the calculation is taking the
time? Is it the global optimisation of all parameters? Are the final
results of each round similar or completely different (selected model
wise and parameter value wise). How do the iteration numbers compare
at each stage. Essentially a fine analysis and comparison of the
results files and the printout from relax will be necessary to track
down this abnormal computation time. Oh, are you running these on the
same computer as the previous analysis?
As for the optimisation algorithm being stuck, if you've used the
default algorithm then this shouldn't happen. Optimisation should
terminate. There are certain very rare situations where the algorithm
known as the GMW Hessian modification, which is used by default as a
subalgorithm by the Newton algorithm in relax, can take large amounts
of time to complete. You'll see this as a increase in the number of
iterations by 4 to 5 orders of magnitude. One way to test this is to
use a lower quality optimisation algorithm first and then complete to
high precision with the Newton algorithm. In this case I would use
simplex first followed by the default Newton algorithm and its default
subalgorithms. In all cases constraints should be used. This will
only solve the long computation times if the GMW algorithm is at
fault.
Regards,
Edward
On 9/4/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
Hi all,
I am using the full_analysis.py script with data a three magnetic fields.
After a first complete cycle (going through the final optimization), I
realized that a few residues had extremely high chi-squared values (>
1000) no matter the diffusion model or model-free model chosen...
So I removed those residues (7 out of 222) and started the full_analysis
protocole again.
However, the optimization times are now extremely long and I should get
the final results in weeks...
Here are the available times (for local_tm, sphere and ellipsoid) :
Diffusion_model Round Time-before_N=222 X2
Time-now_N=215 X2
=============== ===== ================= =======
============== =======
local_tm --- 12h30 45949
14h30 5802 OK, X2 much smaller
sphere init --- 1154338 ---
249255
1 2h30 65654 36h00
10303 Long, but X2 much smaller
2 2h30 65654 > 30h00
ellipsoid init --- 753535
--- 177764
1 4h00 64592 >
67h00 ??
2 2h30 64592
not_there_yet
Is it possible that the algorithms get stuck somewhere during the
optimization..?
I thought that removing badly fit residues would, on the contrary, speed
up calculations...
Thanks for ideas !
Sébastien :)
--
______________________________________
_______________________________________________
| |
|| Sebastien Morin ||
||| Etudiant au PhD en biochimie |||
|||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne |||||
|||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
||| 1-418-656-2131 #4530 |||
|| ||
|_______________________________________________|
______________________________________
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Re: Extremely long optimization times