[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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