Re: Segmentation fault error with 'nan' pressure and energy

From: Sadegh Faramarzi Ganjabad (safaramarziganjabad_at_mix.wvu.edu)
Date: Tue May 30 2017 - 16:48:09 CDT

Richard,

Thanks for quick reply. Yes there are some identical atom coordinates. But
I need it to be so, for alchemy transformation. Is there any way to deal
with it?

Thanks and regards,
Sadegh

On Tue, May 30, 2017 at 5:41 PM, Richard Overstreet <roverst_at_g.clemson.edu>
wrote:

> 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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