[gmx-users] Re: TMD using free energy code

[Landraille]

I have done a test for a TMD between two conformations of a POPC in water
with this mdp file:

define = -DPOSRES_TMD   ; POSRES-TMD defined in the top file and including
only the heavy atom of POPC 
refcoord-scaling = all
cpp                = /usr/bin/cpp
constraints         =  hbonds
constraint_algorithm = LINCS
integrator          =  md
dt                  =  0.002
nsteps              =  50000
nstxout             =  50000
nstvout             =  50000
nstfout             =  0
nstlog              =  500
nstenergy           =  500
nstxtcout           =  500
nstlist             =  5
ns_type             =  grid
coulombtype         =  PME
rlist               =  1
rcoulomb            =  1
rvdw                =  1
; Berendsen temperature coupling 
Tcoupl              =  v-rescale
tau_t               =  0.1 0.1
tc_grps             =  POPC SOL
ref_t               =  300 300
; Pressure coupling 
Pcoupl              =  Parrinello-Rahman
pcoupltype          =  isotropic
tau_p               =  0.5
ref_p               =  1
compressibility     =  4.5e-05
unconstrained_start =  yes
gen_vel             =  no
gen_temp            =  300
gen_seed            =  173529
optimize_fft        =  yes
; free-energy
free_energy              = yes
init_lambda              = 0.0
delta_lambda           = 0

and these commands :
grompp -f TMD.mdp -c begin.gro -p topol.top -o tmd.tpr -n index.ndx -r
begin.gro -rb end.gro
mdrun -v -deffnm tmd

Nevertheless, it doesn't work even with non-zero value for delta_lambda. I
don't know which free energy options I have to modify. Indeed, according to
the manual, the other options are tuned for FEP or TI.

Any help would be greatly appreciated.

Landraille 

PS : I use v4.5.5. Indeed, with the v4.6, mdrun doesn't start and I have the
error message "Function type U-B not implemented in ip_pert".





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