[gmx-users] free energy

[fatemeh ramezani]

Dear gmx-usersI want to calculate free energy of binding of ligand to Au surface in 8 ns simulation. I considered 7 lambda (lambda= 0, 0.2, 0.4, 0.6, 0.8, 0.9, 1) and for every lambda a mdp file. for example lambda-0 mdp file:
title               =  n.pdb restraining
cpp                 =  /lib/cpp
constraints         =  all-bonds
constraint_algorithm = lincs
lincs_order         = 4
lincs_iter          = 1
integrator          =  sd 
dt                  =  0.0008
nsteps              =  2500000
nstcomm             =  100
nstcalcenergy       =  100
nstdhdl             =  100
comm_mode           =  
nstxout             =  5000
nstvout             =  5000
nstfout             =  0
nstlog              =  5000
nstenergy           =  5000
nstlist             =  10
ns_type             =  grid
rlist               =  1.4
;rlistlong           =  2
coulombtype         =  PME
rcoulomb            =  1.4
rcoulomb-switch     =  0.8
rvdw                =  1
vdwtype             =  shift
rvdw-switch         =  0.9
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  6
ewald_rtol          =  1e-5
optimize_fft        =  yes
  
; Berendsen temperature coupling is on in three groups
Tcoupl              =  V-rescale
tau_t               =  0.1       0.1
tc-grps            =  Protein   Non-Protein
ref_t               =  300       300
; Pressure coupling is  on
;Pcoupl              =  berendsen
Pcoupl              =  Parrinello-Rahman
Pcoupltype         =  isotropic
tau_p               =  5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
energygrps          = Protein  Sol 
freezegrps          = AU  AUI       AUC
freezedim           = Y Y Y  Y Y Y  Y Y Y
free-energy         = yes
couple-moltype      = Protein2
init-lambda         = 0
sc-power            = 1
sc-sigma            = 0.3
sc-alpha            = 1
couple-intramol     =  no
couple-lambda1      = vdwq
couple-lambda0      = none
foreign-lambda      = &ALL_LAMBDAS$
As you can see dt= 0.0008, for 8 ns simulation, I should take the nstep of each Lambda 10000 ( or I should divide 8 ns  between 7  Lambda)? In other words, the simulation time for each of the 7 lambda should be 8 ns or every lambda simulation time should be considered so that the total simulation time of lambdas be 8 ns?
I hope I could correctly ask my question. I would greatly appreciate your response to my question.
 Fatemeh Ramezani