[gmx-users] Doubt about g_lie

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

I have used PME in the production runs of my systems for finding Delta G_Binding using g_lie. But many threads on Gromacs forum warn against it and advise to rerun the whole trajectory using Reaction field Zero, but the cutoff for this rerun is not clearly given. Some threads say a cutoff with large cutoff using RF-0 is necessary. Can you please uggest as to what cutoff(Relative to the system) should be given while re-running the trajectory and what all changes have to be done in the original mdp file(which uses PME). Also, a brief explanation for the whole process for the need of the re-run would be beneficial. Following are the changes I made after studying the past threads:
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;; With PME  ;;;                                     | ;; Re-Run without PME ;;
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 ; Neighborsearching                                 |  ; Neighborsearching
  ns_type     = grid      ; search neighboring grid  |  ns_type     = grid      ; search neighboring grid cells
  nstlist     = 5         ; 10 fs                    |  nstlist     = 5         ; 10 fs
  rlist       = 0.9       ; short-range neighborlist |  rlist       = 1.2       ; short-range neighborlist cutoff (nm)                                                                                            
  rcoulomb    = 0.9       ; short-range electrostatic|  rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)
  rvdw        = 1.4       ; short-range van der Waals|  rvdw        = 1.4       ; short-range van der Waals cutoff (in nm)
                                                     |
; Electrostatics                                     | ; Electrostatics
coulombtype     = PME                                | coulombtype  =  Reaction-Field-zero 
                                                     | epsilon_rf      =  0
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Best Regards,

Bhagyesh