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:
------------------------------------------------------------------------------------------------------------------------
;; With PME ;;; | ;; Re-Run without PME ;;
-------------------------------------------------------------------------------------------------------------------------
; 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
---------------------------------------------------------------------------------------------------------------------------
Best Regards,
Bhagyesh
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