[gmx-users] Issue in Steep descent minimization (Free energy calculation)

[Live King]

Hi everyone,


I know this issue has been addressed several times but I couldn't find the
solution for my problem. So, I had to ask here.

I am trying to calculate free energy using martini forcefield. My system
has water, DPPC bilayer and membrane protein embedded in it. After steepest
descent minimization I get the following note/warning.




*"Stepsize too small, or no change in energy.Converged to machine
precision,but not to the requested precision Fmax < 100 " *


I know it means my structure has clashes or my mdp options are not
adequate. I tried to played with all the suggested parameters before. If
more suggestions will be highly appreciated.My mdp file looks like this :-


; Run control
integrator               = steep
nsteps                   = 5000
; EM criteria and other stuff
emtol                    = 100
emstep                 = 0.01
niter                     = 20
nbfgscorr              = 10
; Output control
nstlog                  = 1
nstenergy             = 1
; Neighborsearching and short-range nonbonded interactions
nstlist                  = 1
ns_type                  = grid
pbc                      =  xyz
rlist                      = 1.2
; Electrostatics
coulombtype           = shift
rcoulomb                 = 1.2
rcoulomb_switch          = 0.0
; van der Waals
vdw-type                 = shift
rvdw-switch              = 0.9
rvdw                     = 1.2
; 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 and pressure coupling are off during EM
tcoupl                   = no
pcoupl                   = no
; Free energy control stuff
free_energy              = yes
init_lambda              = 0.0
delta_lambda             = 0
foreign_lambda           = 0.05
sc-alpha                 = 1.3
sc-power                 = 1.0
sc-sigma                 = 0.47
couple-moltype           = Protein  ; name of moleculetype to decouple
couple-lambda0           = vdw-q      ; only van der Waals interactions
couple-lambda1           = none
couple-intramol          = yes
nstdhdl                  = 10
; Generate velocities to start
gen_vel                  = no
; options for bonds
constraints              = h-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm     = lincs
; Do not constrain the starting configuration
continuation             = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 12