Hello, i want to simulate a 128 DPPC molecule, 3655 water molecules but with
25% of DPPE. I replace de 25% of 128 DPPC molecules with DPPE and i'ḿ using the
same forcefield and topology reported by Lemkul in his KALP15 in DPPC tutorial.
When i want to minimize the energy i use the command line: gmx grompp -f
minim.mdp -c dppc-dppe128.pdb -p topol_dppc.top -o em.tp but the following
error appears: Input/output error: minim.mdp. How can i solve it? Is correct to
use the same forcefield and topology? I'm using Gromacs 5.0.4. This in my
minim.mdp file
; 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)
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