From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Oct 21 2016 - 10:49:22 CDT
Wow. NAMD must store the timestep as a signed 32-bit integer. 2^31 = 2147483648, and according to signed 32-bit integers, 2^31 + 1 = -2^31, which is why you are coming up with negative timesteps. If you want to eliminate this, set firsttimestep to 0 for step 22, and adjust the timestep afterward by hand if need be. Is the DCD the same size as the others though? I've never encountered this problem, so I'm not sure if NAMD terminates as soon as it encounters a negative timestep, or if it continues incrementing happily until numsteps is satisfied. If its the latter, the dynamics are still ok, you will just need to account for a negative timestep as you start step 23.
On 10/21/2016 07:28 AM, Götz, Alexander wrote:
I currently face some troubles with NAMD2.10 and my simulation systems. The systems (I have three nearly equal membrane systems) have all run for 2.1µs in 21 chunks of 100ns (all atom CHARMM36, 2fs integration timestep). Everything worked perfectly fine until step 22. Whenever I want to start step 22 for any of my systems I get the following error in the NAMD output:
TCL: Running for 50000000 steps
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 2100000000 1866.2220 9802.6548 6896.3270 78.1218 -103131.8273 3410.1396 0.0000 0.0000 26331.7058 -54746.6563 301.5845 -81078.3620 -54571.7237 301.5845 -263.9492 -261.2014 396913.4892 -263.9492 -261.2014
OPENING EXTENDED SYSTEM TRAJECTORY FILE
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP -2144967296
CLOSING EXTENDED SYSTEM TRAJECTORY FILE
WRITING COORDINATES TO OUTPUT FILE AT STEP -2144967296
COORDINATE DCD FILE <path removed by the author> WAS NOT CREATED
The last position output (seq=-2) takes 0.006 seconds, 1399.262 MB of memory in use
WRITING VELOCITIES TO OUTPUT FILE AT STEP -2144967296
The last velocity output (seq=-2) takes 0.004 seconds, 1400.191 MB of memory in use
WallClock: 4.380243 CPUTime: 4.380243 Memory: 1400.191406 MB
[Partition 0][Node 0] End of program
I am quite confused about this, because I changed nothing in my NAMD configuration files except for the file numbering of the restart and output files and these are fine (checked by 3 different people). ?For me the problem seems to be related with generation of the DCD file. For the cluster part, the file system of the cluster (IBM GPFS) should be fine because other jobs with equal configurations are working and there has not been any maintenance that could be in relation to the observed problems. In addition step 21 of one of the system worked properly while step 22 of the other two systems failed at the same time. Looks a little bit like 22 is a magic number?
Furthermore, the negative step number in the output, which is not in a line with the run steps, is also quite mysterious for me. I hope anybody has a tip or a solution for me because I have checked nearly everything that came into my mind until now.
Alexander Götz, M.Sc.
Technische Universität München // Fakultät für Physik
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