From: Gareth Price (garethprice_at_me.com)
Date: Sat Apr 13 2013 - 13:52:01 CDT
Hello
I am following the NAMD tutorial (http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node9.html) to minimise my protein in a water box. When I run the actual NAMD program, with the attached conf.namd file, it quite quickly exits with the attached log file. Most importantly it terminates with:
LDB: ============= START OF LOAD BALANCING ============== 340.786
LDB: Largest compute 179 load 8.530063 is 10.0% of average load 85.194022
LDB: Average compute 2.082990 is 2.4% of average load 85.194022
LDB: TIME 340.792 LOAD: AVG 85.194 MAX 131.415 PROXIES: TOTAL 24 MAXPE 7 MAXPATCH 3 None MEM: 3310.88 MB
LDB: TIME 340.797 LOAD: AVG 85.194 MAX 92.1218 PROXIES: TOTAL 24 MAXPE 7 MAXPATCH 3 TorusLB MEM: 3310.88 MB
LDB: ============== END OF LOAD BALANCING =============== 340.799
Info: useSync: 1 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 340.992
LINE MINIMIZER BRACKET: DX 1.62127e-09 1.002e-09 DU -5288.41 240.855 DUDX -1.1042e+14 -1.09678e+14 -1.09218e+14
PRESSURE: 100 1.33313e+09 -1.009e+07 3.3175e+07 -1.009e+07 1.29659e+09 -775795 3.3175e+07 -775795 1.34968e+09
GPRESSURE: 100 1.42554e+09 -9.55804e+06 3.11602e+07 -6.61256e+06 1.38876e+09 -4.2318e+06 3.10716e+07 586571 1.44297e+09
Info: Initial time: 4 CPUs 3.23398 s/step 18.7151 days/ns 2533.11 MB memory
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 100 933457.0735 200198.1313 8171.3299 38969.5390 -67311.8822 351142159.9599 0.0000 0.0000 0.0000 352255644.1514 0.0000 352255644.1514 352255644.1514 0.0000 1326464790.2855 1419090028.9051 74088.0000 1326464790.2855 1419090028.9051
REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN.
TCL: Running for 2500 steps
ERROR: Constraint failure in RATTLE algorithm for atom 469!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 795!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 202!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 620!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 22!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 792!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 36!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
====================================================
I'm at an absolute loss as to why this is happening. I
Could someone help me with this, please?
I note that the initial values that are outputted in the log are very high - is this the reason?
I have also found that this is talked about a bit in the WIKI, http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdTroubleshooting, but nothing I do (in terms of adding margin, bigger PME box etc) is helping!
Thanks for your time,
Gareth
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