From: SM Bargeen A Turzo (s.turzo_at_vikes.csuohio.edu)
Date: Sun Apr 29 2018 - 22:36:54 CDT
Hi
I am running to this energy minimization error, where I am getting the following error[1]. The weird part is, I created the input files using vmd's qwikmd plugin and I have successfully simulated the wildtype protein for 5ns without any error. However when I mutate certain residues I run into this error. I was wondering if anyone can help me understand why am I getting this certain error, it would be really helpful. Any help is greatly appreciated. The full log and the conf file can be found here[2]. Let me know if I need to provide any other files regarding this matter.
-Bargeen
-------------
[1]
MINIMIZER STARTING CONJUGATE GRADIENT ALGORITHM
LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
------------- Processor 82 Exiting: Caught Signal ------------
Signal: segmentation violation
Suggestion: Try running with '++debug', or linking with '-memory paranoid' (memory paranoid requires '+netpoll' at runtime).
------------- Processor 54 Exiting: Caught Signal ------------
Signal: segmentation violation
Suggestion: Try running with '++debug', or linking with '-memory paranoid' (memory paranoid requires '+netpoll' at runtime).
[54] Stack Traceback:
[54:0] [0xe3c50f]
[54:1] [0xb5fcc0]
[54:2] [0xf3fe7e]
[54:3] [0x1283ab0]
[54:4] [0x14515b7]
[54:5] [0x52a690]
[54:6] [0x51e6b2]
[54:7] __libc_start_main+0xfd [0x3af8c1ed1d]
[54:8] [0x40fe89]
Fatal error on PE 54> segmentation violation
[comet-20-07.sdsc.edu:mpirun_rsh][signal_processor] Caught signal 15, killing job
[https://r1.res.office365.com/owa/prem/images/dc-generic_40.png]<https://csuohio-my.sharepoint.com/:f:/g/personal/2681093_vikes_csuohio_edu/EoMuQiJopcBOtYjFbsOhsg0B-AyHZvzt3uWoJPB9tY5P2g?e=0nd63Y>
Min_error<https://csuohio-my.sharepoint.com/:f:/g/personal/2681093_vikes_csuohio_edu/EoMuQiJopcBOtYjFbsOhsg0B-AyHZvzt3uWoJPB9tY5P2g?e=0nd63Y>
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