<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><br>Dear All,</div><div> </div><div>The first mini.mdp is as following:</div><div><br> </div><pre>; 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                = 1<var id="yui-ie-cursor"></var>000.0         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)
</pre><pre> </pre><pre>The second mini.mdp is as folowing:</pre><pre><pre>; 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
</pre><pre> </pre><pre>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?</pre><pre>Suppose I use AMBER 99SB force field, will you lease tell me how can decide the value of the above cut-offs?</pre><pre> </pre><pre>Cheers,</pre><pre><font>Acoot</font></pre><pre> </pre></pre></div></body></html>