On 4/19/20 2:43 PM, Elham Taghikhani 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

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 
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 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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