[gmx-users] segmentation fault core dumped

[Najamuddin Memon]

First of all optimize the geometry of protein by using wincoot especially
considering your respective atom/molecule/amino acid
Change the algorithm of energy minimization to conjugate gradient
If you can see the respective atom it is in collision with any other atom
in any visualization tool. This can be resolved by using wincoot



On Thu, Nov 14, 2019, 4:18 PM Yogesh Sharma <yogesh.rma13 at gmail.com> wrote:

> Greetings everyone
>
> I was following protein ligand complex tutorial.
>
> 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.
>
> 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.
>
>  *  with  regards*
> *Yogesh Sharma*
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