Previous Thread
Next Thread
Print Thread
Segmentation failure when loading GBSW parameters
#37298 01/24/19 09:25 AM
Joined: Jan 2019
Posts: 56
P
pmj Offline OP
Forum Member
OP Offline
Forum Member
P
Joined: Jan 2019
Posts: 56
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!

Last edited by pmj; 01/24/19 02:15 PM.
Re: Segmentation failure when loading GBSW parameters
pmj #37299 01/24/19 06:22 PM
Joined: Sep 2003
Posts: 8,447
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,447
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

Re: Segmentation failure when loading GBSW parameters
pmj #37302 01/25/19 08:14 AM
Joined: Jan 2019
Posts: 56
P
pmj Offline OP
Forum Member
OP Offline
Forum Member
P
Joined: Jan 2019
Posts: 56
Dear Rick,

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

Thanks!

Re: Segmentation failure when loading GBSW parameters
pmj #37303 01/25/19 09:45 AM
Joined: Sep 2003
Posts: 4,771
Likes: 2
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,771
Likes: 2
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

Moderated by  John Legato, lennart 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.010s Queries: 22 (0.003s) Memory: 0.9117 MB (Peak: 0.9933 MB) Data Comp: Off Server Time: 2020-05-28 20:42:42 UTC
Valid HTML 5 and Valid CSS