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

[Elham Taghikhani]

Hi
As you said I checked my structure for any bad contact, but the close atoms are part of the protein so I can't delete them to minimize the structure. And water molecules are not that much close to make bad contact with the atom.
And the atom which errored  during minimization it's the atom that bound covalently to a ligand. I think there is something wrong with the bond length between N of amino acid and the C of the ligand. How can I find the correct bond length? 


> On Apr 20, 2020, at 1:08 AM, Elham Taghikhani <elham802011 at yahoo.com> wrote:
> 
> 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.
>>