[gmx-users] Segmentation fault (core dumped) error during minimization

[Justin Lemkul]

On 4/19/20 2:43 PM, Elham Taghikhani wrote:
> Hi
>   I am simulating a protein-ligand system, using oplss force field but i got this error during minimization.
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =        50000
> Step=    0, Dmax= 1.0e-02 nm, Epot=  1.27151e+33 Fmax= 4.76291e+07, atom= 1996

Look for bad contacts around atom 1996.

> Segmentation fault (core dumped)
>
> and this is my mpd file:; LINES STARTING WITH ';' ARE COMMENTS
> title		    = Minimization	; Title of run
>
> ; Parameters describing what to do, when to stop and what to save
> integrator	    = steep		; Algorithm (steep = steepest descent minimization)
> emtol		    = 1000.0  	; Stop minimization when the maximum force < 10.0 kJ/mol
> emstep          = 0.01      ; Energy step size
> nsteps		    = 50000	  	; Maximum number of (minimization) steps to perform
>
> ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
> nstlist		    = 1		        ; Frequency to update the neighbor list and long range forces
> cutoff-scheme   = Verlet
> ns_type		    = grid		    ; Method to determine neighbor list (simple, grid)
> rlist		    = 1.2		    ; Cut-off for making neighbor list (short range forces)
> coulombtype	    = PME		    ; Treatment of long range electrostatic interactions
> rcoulomb	    = 1.2		    ; long range electrostatic cut-off
> vdwtype         = cutoff
> vdw-modifier    = force-switch
> rvdw-switch     = 1.0
> rvdw		    = 1.2		    ; long range Van der Waals cut-off
> pbc             = xyz 		    ; Periodic Boundary Conditions
> DispCorr        = no
> Can anyone suggest how to troubleshoot this error?

Your cutoffs are for the CHARMM force field, not OPLS. This isn't the 
source of the error, but you are using the force field incorrectly.

Other than that, protein-ligand complexes are specifically addressed in 
the troubleshooting section of 
http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system

-Justin

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Justin A. Lemkul, Ph.D.
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