From: Richard Overstreet (roverst_at_g.clemson.edu)
Date: Tue May 30 2017 - 16:41:33 CDT
I would check if atom coordinates are identical.
-Richard
On 05/30/2017 05:17 PM, Sadegh Faramarzi Ganjabad wrote:
> Dear NAMD users,
>
> I have seen couple of posts with the same topic, but still can't
> figure it out. I am trying to minimize a membrane protein system prier
> to run FEP/TI calculations. So, a part of my protein has a dual
> topology. I get 'Segmentation fault' with no further explanation. In
> my log file there are 'not a number, nan' values for pressure and
> energy. Here is a part of my log file
>
> ETITLE: TS BOND ANGLE DIHED IMPRP
> ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL
> TOTAL3 TEMPAVG PRESSURE GPRESSURE
> VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 10 2846.5220 11429.2936 nan 185.1025
> -94079.6680 9999999999.9999 0.0000 0.0000
> 0.0000 nan 0.0000 nan
> nan 0.0000 nan nan 450474.3936
> nan nan
>
> MINIMIZER SLOWLY MOVING 4 ATOMS WITH BAD CONTACTS DOWNHILL
> PRESSURE: 11 nan nan nan nan nan nan nan nan nan
> GPRESSURE: 11 nan nan nan nan nan nan nan nan nan
> ENERGY: 11 3035.3700 11458.4002 nan 185.3481
> -94074.5040 9999999999.9999 0.0000 0.0000
> 0.0000 nan 0.0000 nan
> nan 0.0000 nan nan 450474.3936
> nan nan
>
> MINIMIZER SLOWLY MOVING 4 ATOMS WITH BAD CONTACTS DOWNHILL
> PRESSURE: 12 nan nan nan nan nan nan nan nan nan
> GPRESSURE: 12 nan nan nan nan nan nan nan nan nan
> ENERGY: 12 3266.8947 11491.0698 nan 185.6188
> -94067.9283 9999999999.9999 0.0000 0.0000
> 0.0000 nan 0.0000 nan
> nan 0.0000 nan nan 450474.3936
> nan nan
>
> MINIMIZER STARTING CONJUGATE GRADIENT ALGORITHM
> LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
>
>
> There is nothing special about my configuration file. I have tested it
> on other systems and it works file. Does anybody has a clue to this issue?
>
> Thanks,
> Sadegh
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