[gmx-users] about using restraint-lambdas and bonded-lambda

[Qasim Pars]

Dear users,

I would use the following free energy parameters in the mdp files but I am
confused about using restraint-lambdas and bonded-lambdas in the mdp files.
Do you think that I should add restraint-lambdas and bonded-lambdas into
mdp files as well? Do they have the big effect on the accuracy of the free
energy results? Please look at the intermolecular_interactions part below
in top file also.

; Free energy control parameters
free-energy              = yes
couple-moltype           = ligand
couple-lambda0           = vdw-q
couple-lambda1           = none
couple-intramol          = no
sc-alpha                 = 0.5
sc-power                 = 1
sc-sigma         = 0.3
init-lambda-state        = 0
coul-lambdas             = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.00
1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0
1.00 1.0
vdw-lambdas              = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.05
0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9
0.95 1.0
nstdhdl                  = 100
dhdl-print-energy        = yes
calc-lambda-neighbors    = -1


Here is the intermolecular_interactions part in the top file:
[ intermolecular_interactions]
; distance restraints
[ bonds ]
;    i     j  type     r0A     r1A     r2A    fcA    r0B     r1B     r2B
fcB
  2141  1656    10     0.609   0.609   10.0   0.0    0.609   0.609   10.0
4184.000

[ angle_restraints ]
;   ai    aj    ak    al  type    thA      fcA    multA  thB      fcB
multB
  1658  1656  2141  1656     1    91.04    0.0    1    91.04    41.840    1
  1656  2141  2140  2141     1   109.88    0.0    1   109.88    41.840    1

[ dihedral_restraints ]
;   ai    aj    ak    al  type    phiA     dphiA  fcA    phiB      dphiB
fcB
  1668  1658  1656  2141     1    157.98   0.0    0.0    157.98    0.0
41.840
  1658  1656  2141  2140     1    -123.02   0.0    0.0    -123.02    0.0
41.840
  1656  2141  2140  2136     1    165.76   0.0    0.0    165.76    0.0
41.840


Thanks in advance

-- 
Qasim Pars