[gmx-users] FEP: mdp setting for mutation

[Alex Mathew]

Hi,

Following changes are made in the mdp file for mutation analysis.Can anyone
tell me is there anything wrong here?



; init_lambda_state        0    1    2    3    4    5    6    7    8    9
 10   11   12   13   14   15   16   17   18   19   20
vdw_lambdas              = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
coul_lambdas              = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00

bonded_lambdas           = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
restraint_lambdas          = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00

mass_lambdas               = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00

temperature_lambdas      = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Options for the decoupling
sc-alpha                 = 0.5
sc-coul                  = yes      ; linear interpolation of Coulomb (none
in this case)
sc-power                 = 1
sc-sigma                 = 0.3
;couple-moltype           = Methane  ; name of moleculetype to decouple
;couple-lambda0           = vdw      ; only van der Waals interactions
;couple-lambda1           = none     ; turn off everything, in this case
only vdW
;couple-intramol          = no
nstdhdl                  = 10