From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Jan 30 2017 - 01:44:14 CST
I’d just suppose a random memory error, try if restarting from the .old restart solves the problem.
Von: Mohaddeseh Habibzadeh [mailto:m.habibzadeh_at_azaruniv.edu]
Gesendet: Samstag, 28. Januar 2017 20:24
An: norman.geist_at_uni-greifswald.de
Betreff: Re: AW: AW: namd-l: not a number in NAMD log file
Hello
I'm sorry replying late!
The nans started to occur later during the simulation, after 200 or more frames.
Sincerely
On Wed, 01/18/2017 09:01 AM, Norman Geist < <mailto:norman.geist_at_uni-greifswald.de> norman.geist_at_uni-greifswald.de> wrote:
Did the nans start to occur later during the simulation or right from the start?
Von: Mohaddeseh Habibzadeh [mailto:m.habibzadeh_at_azaruniv.edu]
Gesendet: Mittwoch, 18. Januar 2017 13:45
An: Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> >; namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
Betreff: Re: AW: namd-l: not a number in NAMD log file
Hi
Is this reproducible?
Yes, It happened for all 5 times I tested.
Do you have a precompiled NAMD bult or compiled on your own? It is compiled
What OS are you running? Linux, Debian
Are you running on GPUs? yes,
What happens if you just continue from the last restart files?
In all steps I used the last step's restart file. (xsc, pdb, coor all for previous step)
Thank you very much
On Wed, 01/18/2017 02:14 AM, Norman Geist < <mailto:norman.geist_at_uni-greifswald.de> norman.geist_at_uni-greifswald.de> wrote:
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> [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Mohaddeseh Habibzadeh
Gesendet: Dienstag, 17. Januar 2017 07:32
An: <mailto:namd-l_at_ks.uiuc.edu> 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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