[gmx-users] on 2 different mini.mdp file

[Acoot Brett]

Dear All,
 
The first mini.mdp is as following:

 
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
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
ns_type		= grid		; Method to determine neighbor list (simple, grid)
rlist		= 1.0		; Cut-off for making neighbor list (short range forces)
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 second mini.mdp is as folowing:
; 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       = 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
ns_type     = grid      ; Method to determine neighbor list (simple, grid)
rlist       = 1.4       ; Cut-off for making neighbor list (short range forces)
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 
 
The difference is the cut-off. One is 1.4,the other is 1.0. Can anyone explain their difference on the influence of the MD result?
Suppose I use AMBER 99SB force field, will you lease tell me how can decide the value of the above cut-offs?
 
Cheers,
Acoot
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