[gmx-users] Need help for the free energy calculation.

[Rui Zhang]

Dear all,
I am doing the free energy calculation using Gromacs 4.6.4 now. However, I
got the message by g_bar:
-----------
Program g_bar, VERSION 4.6.4
Source code file: /home/rui/Downloads/gromacs-4.6.4/src/tools/gmx_bar.c,
line: 1208

Fatal error:
Could not find a set for foreign lambda = 0.000000
in the files for lambda = 0.000000
---------

Could anyone help me to resolve this problem. Please also see my mdp input:
---------------------------

; Run control
integrator               = sd

; Parameters describing what to do, when to stop and what to save
nsteps        = 5000000    ; Maximum number of (minimization) steps to
perform 12000ns
dt              = 0.002         ; 2fs

; Output control
cutoff-scheme            = group
nstlog                   = 100
nstenergy                = 10
nstcalcenergy             = 10
; Neighborsearching and short-range nonbonded interactions
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.2

; Electrostatics
coulombtype              = PME
rcoulomb                 = 1.2

; van der Waals
vdw-type                 = cut-off
;rvdw-switch              = 0.9
rvdw                     = 1.2
;vdw-modifier=Potential-shift-Verlet

; Apply long range dispersion corrections for Energy and Pressure
DispCorr                  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12

; EWALD/PME/PPPM parameters
pme_order                = 6
ewald_rtol               = 1e-06
epsilon_surface          = 0
optimize_fft             = no

;Temperature coupling
tcoupl=V-rescale               ;berendsen
tc_grps=Protein CA2+_Water_and_ions
tau_t=0.1 0.1;ps time constant for coupling for each group
ref_t=300 300;K reference temperature

; Pressure coupling
pcoupl = Parrinello-Rahman
Pcoupltype=isotropic
tau_p=0.5
ref_p=1.0
compressibility=4.5e-5
refcoord_scaling=com

; Free energy control stuff
free_energy              = yes
init_lambda              = 0.1
init-lambda-state     = -1
delta_lambda             = 0
fep-lambdas              = 0 0.2
;coul-laambdas
couple-intramol          = yes
sc-alpha                 = 0.5
sc-power                 = 1.0
sc-sigma                 = 0.3
nstdhdl                  = 10

; Generate velocities to start
gen_vel                  = no

; Type of constraint algorithm
constraints              = h-bonds
constraint-algorithm     = lincs
continuation             = yes
ld_seed             =-1
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 12

; Output control
nstxout                  = 1000   ; frequency to write coordinates to
output trajectory file
;energygrps    =  Protein;  Which energy group(s) to write to disk
------------
Thank you very much for any help!
Sincerely,

Rui Zhang


-- 

Dr. Rui Zhang
Postdoctoral Research Associate
Department of Veterinary Pathobiology
Texas A&M University
College Station, TX 77840
rzhan001 at tamu.edu
(305) 301-7879