Re: AW: not a number in NAMD log file

From: Mohaddeseh Habibzadeh (m.habibzadeh_at_azaruniv.edu)
Date: Wed Jan 18 2017 - 06:44:58 CST

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 <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] 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

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:00 CST