From: Mohaddeseh Habibzadeh (m.habibzadeh_at_azaruniv.edu)
Date: Tue Jan 17 2017 - 00:31:55 CST
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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