[gmx-users] segmentation fault core dumped

[Justin Lemkul]

On 11/14/19 6:17 AM, Yogesh Sharma wrote:
> Greetings everyone
>
> I was following protein ligand complex tutorial.

Given the atom names listed below, you're not doing the tutorial but 
perhaps are trying to follow its method? There's a big difference. If 
you're doing something different, you need to provide us with all 
relevant details - what the system is, how you parametrized and 
validated the ligand topology, etc.

> EM run was fine even with double precision.
>
> Steepest Descents converged to Fmax < 1000 in 101 steps
> Potential Energy  = -2.71399964872904e+06
> Maximum force     =  9.15885947946535e+02 on atom 4411
> Norm of force     =  1.98296351352040e+01
>
> But when I proceeded to nvt or npt equlibriation run. I am getting
>
> starting mdrun 'SOL'
> 50000 steps,    100.0 ps.
>   segmental fault core dumped.
>
> To troubleshoot I checked .gro file for atom 4411.
>
> 459TRP    NE1 4411   5.806   5.696   4.267
>
> 33678SOL     OW 4411   5.925  11.717   8.738
>
> I am attaching picture here for 4411 atom containing residues for reference.

The mailing list does not accept attachments.

> Both of the atoms are inside box parameters.
>
>   I even decreased temperature to 1K  or  30K but all in vain
>
> Can you help me with this? Thank you.

Does the system work without the ligand? Is the ligand topology of 
sufficient quality or (if you're using CGenFF as implied by the mention 
of the tutorial above) are there penalties that you need to address 
before proceeding?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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