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#37298 - 01/24/19 04:25 AM Segmentation failure when loading GBSW parameters
pmj Online   content
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Registered: 01/15/19
Posts: 11
Dear all,

I am using free version of CHARMM, which I downloaded one week ago. In my system I have around 70K atoms, but I am using implicit solvation model GBSW.

I compiled CHARMM with ./install.com gnu xxlarge x86_64.

When I test each protein chain or nucleic acid chain separately, I am able to reach the stage when I would do dynamics. However, when I use entire system, it fails after he reads some of the GBSW radii parameters.

The error I get is related to SIGSEGV segmentation fault - invalid memory reference.

I was wondering what does usually cause this errors?

Obviously, I can attach my input and output, but I have many files, so if you could just give me your insights without it I would appreciate it.

I was wondering if GBSW was configured to this size of the system in the free version?

Thank you!


Edited by pmj (01/24/19 09:15 AM)

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#37299 - 01/24/19 01:22 PM Re: Segmentation failure when loading GBSW parameters [Re: pmj]
rmv Online   content

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Registered: 09/17/03
Posts: 8290
Loc: 39 03 48 N, 77 06 54 W
Unfortunately, there can be numerous causes of a segmentation fault, including bad input and bad source code. Sometimes, there can be an error or warning earlier in the output log file; you should examine the output in more detail for additional clues.

Please see the READ BEFORE POSTING topic for guidelines on posting output logs as .txt attachments.
_________________________
Rick Venable
computational chemist


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#37302 - 01/25/19 03:14 AM Re: Segmentation failure when loading GBSW parameters [Re: pmj]
pmj Online   content
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Registered: 01/15/19
Posts: 11
Dear Rick,

I managed to solve my issue by reducing the values of nonbonded terms.

Thanks!

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#37303 - 01/25/19 04:45 AM Re: Segmentation failure when loading GBSW parameters [Re: pmj]
lennart Offline

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Registered: 09/25/03
Posts: 4700
Loc: ~ 59N, 15E
It may be that there is an error check missing in the code, but we cannot fix it since we only have a vague description of what happened.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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