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

[Elham Taghikhani]

Thank you
I corrected the mdp file. As you said I opened my gro file in VMD but I didn't notice any bad contact around the atom.
Could you explain how can I observe bad contacts in the structure?
I even tried the different box size but it didn't work.
Both ligand and protein are ok with minimization separately.


> On Apr 19, 2020, at 11:13 PM, Elham Taghikhani <elham802011 at yahoo.com> 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
> 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? 
> The system is nuetralized.
>  
> Thank you in advance.
>