From: Collin Nisler (cnisler_at_uchicago.edu)
Date: Mon Dec 05 2022 - 13:52:59 CST
Hello NAMD mailing list, I am running an SMD simulation in which I am applying a restoring force to the membrane (using the SMD implementation with a velocity of 0) to the center of mass of the lipid head groups. I am doing this for several systems, and have had no trouble with any of them until now. When I try and restart one particular system, I am getting a large discontinuity in the reported SMD force in the log file. I have quadruple checked the configuration file, and the outputs of the previous run, and they are all fine. The first timestep of the new run is the same as the final of the previous run, but the force is off by ~6-8 pN and the position of the center of mass is not equivalent. I tried restarting from the .old files, but encounter the same issue. Visually, there does seem to be a slight but sudden change in the volume of the system from the .restart.coor of the previous run to the first frame of the new run that is larger than a typical volume fluctuation, but I am uncertain what could be causing it. Any assistance with this issue would be greatly appreciated.
Collin
P.S. - if it helps, here are the outputs of the SMD and energies from the previous and the new run, respectively:
SMD 9999000 0.896833 6.2692 -2.32739 0 0 10.7401
PRESSURE: 9999000 -119.373 -62.9759 2.71343 -62.9724 -330.815 134.662 1.96508 134.588 63.6457
GPRESSURE: 9999000 -94.4046 -119.42 48.8395 -87.1822 -261.346 126.312 -21.7714 23.3959 65.3098
PRESSAVG: 9999000 0.404245 -17.2165 -9.78987 -17.2132 -41.7086 -1.97229 -10.5398 -2.03962 35.7783
GPRESSAVG: 9999000 -0.38485 -15.0718 -10.9276 -22.4012 -41.3157 -0.805085 -8.33718 -2.6313 36.1118
TIMING: 9999000 CPU: 38712, 0.00382879/step Wall: 38712, 0.00382879/step, 0.00106355 hours remaining, 6381.093750 MB of memory in use.
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC
TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 9999000 4040.3011 21372.0753 14009.8765 351.8909 -577222.3282 34162.8347 0.0000 0.0000 86932.2595
-416353.0902 299.5748 -503285.3497 -415888.9616 300.6816 -128.8473 -96.8136 1352096.2117 -1.8420 -1.8629
SMD 9999000 1.4546 0.216995 -2.23659 0 0 4.43131
PRESSURE: 9999000 -117.942 -65.6161 -0.164887 -65.6126 -325.462 139.296 -0.914919 139.172 74.1378
GPRESSURE: 9999000 -94.2021 -119.566 49.4876 -87.33 -261.28 126 -21.1207 23.0414 65.6589
ENERGY: 9999000 4040.3011 21372.0753 14009.8765 351.8909 -577222.1043 34162.8347 0.0000 0.0000 86895.5580 -416389.5679 299.4483 -503285.1259 -415907.7907 299.4483 -123.0888 -96.6077 1352096.2117 -123.0888 -96.6077
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