On 4/19/20 4:38 PM, Elham Taghikhani 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?

Calculate interatomic distances and look for anything very close to atom 1996, check the topology to make sure sensible interactions will occur between that atom and its surroundings.

I even tried the different box size but it didn't work.

Box size is not relevant here.


Both ligand and protein are ok with minimization separately.

On Apr 19, 2020, at 11:13 PM, Elham Taghikhani <elham802...@yahoo.com> wrote:

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:
title               = Minimization      ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator          = steep             ; Algorithm (steep = steepest descent 
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.


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

jalem...@vt.edu | (540) 231-3129


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