[gmx-users] a question related to minim.mdp

[Brett]

Dear all,


Following is a minim.mdp from the website, in which "nsteps      = 50000".


Here what I want to ask is, does it mean the larger the protein, the larger the value of nsteps? Or for any size of protein regardless of mw, as for it has specified "emtol       = 500.0",  " nsteps      = 50000" will always work?


Brett


minim.mdp was as following,

"; ions.mdp - used as input into grompp to generate ions.tpr 
; Parameters describing what to do, when to stop and what to save 
integrator  = steep     ; Algorithm (steep = steepest descent minimization) 
emtol       = 500.0    ; 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    = 1.4       ; Short-range electrostatic cut-off 
rvdw        = 1.4       ; Short-range Van der Waals cut-off 
pbc         = xyz       ; Periodic Boundary Conditions"