AW: not a number in NAMD log file

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Jan 18 2017 - 01:14:12 CST

Hi,

 

Some more questions that might bee answered to give advice:

 

Is this reproducible?

Do you have a precompiled NAMD bult or compiled on your own?

What OS are you running?

Are you running on GPUs?

What happens if you just continue from the last restart files?

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Mohaddeseh Habibzadeh
Gesendet: Dienstag, 17. Januar 2017 07:32
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: not a number in NAMD log file

 

​Hi dear NAMD users
I had 3 minimizations on the RNA molecule (with 1088 atoms + 50 ions) with weak restraint on RNA and the ions, before starting I measured the box size and put in the first min config file, after that I heated up the system to 310 K. (with void formation!)
Then I ran a nvt md in order to equilibrate the system after heating, first with constraint on RNA an then a 6ns nvt without constraint.
Finally I was running npt of the whole system, bubbles disappeared but in frame 206 in the log file I saw -nan and I stopped the run. ( If more information is needed tell me, please )
Can anyone help me with this?
Any help would be appreciated.

This is part of my log file:

LDB: TIME 19245 LOAD: AVG 0.442106 MAX 0.449301 PROXIES: TOTAL 40 MAXPE 14 MAXPATCH 3 RefineTorusLB MEM: 268.879 MB
LDB: TIME 19245 LOAD: AVG 0.442106 MAX 0.449301 PROXIES: TOTAL 40 MAXPE 14 MAXPATCH 3 RefineTorusLB MEM: 268.879 MB
LDB: ============== END OF LOAD BALANCING =============== 19245
Info: useSync: 0 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 19245
ENERGY: 2250000 -nan -nan nan nan -nan -nan 0.0000 0.0000 nan nan nan -nan -nan nan -nan -nan -nan -nan -nan

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 2250000
WRITING COORDINATES TO DCD FILE md-final-npt.dcd AT STEP 2250000

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