[gmx-users] ERROR MESSAGE DURING MINIMIZATION

Omamuyovwi Akemu omamuyovwiakemu at yahoo.com
Fri Jul 29 08:41:04 CEST 2016


Dear Gromacs Users,
I am trying my first simulation just by following the tutorial available by benvan lab 
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html).However, I encountered an error message during the minimization stage.I will appreciate any comment that can resolve this error. 
Below are the em.mdp file ( available online )  and error message:
; minim.mdp - used as input into grompp to generate em.tpr
integrator      = steep         ; Algorithm (steep = steepest descent minimization)
emtol           = 1000.0        ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
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)
coulombtype         = PME               ; Treatment of long range electrostatic interactions
rcoulomb            = 1.0               ; Short-range electrostatic cut-off
rvdw                = 1.0               ; Short-range Van der Waals cut-off
pbc                     = xyz           ; Periodic Boundary Conditions (yes/no)


The error message is:GROMACS:      gmx grompp, VERSION 5.1.2
Executable:   /home/omamu/GROMACS/gromacs-5.1.2/build/bin/gmx
Data prefix:  /home/omamu/GROMACS/gromacs-5.1.2 (source tree)
Command line:
  gmx grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr


-------------------------------------------------------
Program:     gmx grompp, VERSION 5.1.2
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
Function:    void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -f
    File 'minim.mdp' does not exist or is not accessible.


Thank you.

Jolayemi OmamuyovwiUniversity of Benin,Nigeria.



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