Re: Energy Minimization failure for mutants

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Mon Apr 30 2018 - 09:24:35 CDT

Dear Bargeen,

As a general procedure before starting any simulation, I would suggest
inspecting the system that you are about to simulate. Especially if you
have any sort of manipulation, like a mutation. Check if the confirmation
look sane, and you may make some measurements, like atoms' distance to make
sure that your structure is not too bad. Of course, some abnormalities will
be fixed during the minimization and equilibration, but others will not,
and it might need some additional manipulation before simulation. QwikMD,
like many other automated structure manipulation tools, tries to prevent
most of these issues, but it can fail.

Now on the NAMD side, you might want to run your minimization on a local
machine before you send to a cluster. You save queue time by checking if
the simulation runs before submitting the job. Also, running the
minimization on a smaller machine (or smaller node count) may avoid
communications issue that might surge from a not so optimal structure.

Best

João

On Sun, Apr 29, 2018 at 10:42 PM SM Bargeen A Turzo <
s.turzo_at_vikes.csuohio.edu> wrote:

> 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
>
>
> [2]
> https://csuohio-my.sharepoint.com/:f:/g/personal/2681093_vikes_csuohio_edu/EoMuQiJopcBOtYjFbsOhsg0B-AyHZvzt3uWoJPB9tY5P2g?e=0nd63Y
>
> <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>
> Shared via OneDrive
>
>
>

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851

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