[gmx-users] InflateGRO methodology deletion radius

Shima Arasteh shima_arasteh2001 at yahoo.com
Sat Jun 15 09:56:28 CEST 2013


In Kalp15_DPPC tutorial, when the InflateGRO methodology is applied to pack the lipids, I need to follow the iteration while the cutoff value changed to 0.
I' d like to know what settings of EM.mdp file are suggested to get the best results of doing shrinking steps?
When I set the settings as follow, the lipids interfere the peptide however the APL doesn't get the experimental value. So the configuration is not ideal to get through the equilibrium steps.

define         = -DPOSRES
integrator    = steep        ; Algorithm (steep = steepest descent minimization)
emtol        = 100.0      ; Stop minimization when the maximum force < 100.0 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        = 0.4    ; Cut-off for making neighbor list (short range forces)
rlistlong       = 6.0
coulombtype    = PME        ; Treatment of long range electrostatic interactions
rcoulomb    = 0.4        ; Short-range electrostatic cut-off
rvdw        = 0.4        ; Short-range Van der Waals cut-off
vdwtype         = switch
rvdw_switch     = 0.2
pbc        = xyz         ; Periodic Boundary Conditions

Now, I am wondering if such a settings will serve a proper deletion radius?


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