[gmx-users] free energy blank dgdl

[Moeed]

Hello Justin

Thanks for your attention. Just to remind you: I am getting blank dgdl and I
found this in log file:

> There are 0 atoms and 0 charges for free energy perturbation


====================================
EM
>
> grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr >&
> output.grompp_em
>
> mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g  em-l0.log -e em-l0.edr
> -v >& output.mdrun_em
>
> MD
>
> grompp -f md-l0.mdp -c em-l0.gro -p PE60-0c-itp.top -o md-l0.tpr -n
> PE-HEX.ndx>& output.grompp_md
>
> mdrun -s md-l0.tpr -o md-l0.trr -c md-l0.gro -g md-l0.log -e md-l0.edr
> -x md-l0.xtc -dgdl md-l0.dgdl -v >& output.mdrun_md
================================
with mdp :


pbc              =  xyz
energygrps          =  PE HEX

;        Run control
integrator          =  md
dt                  =  0.002
nsteps              =  500000 ;5000
nstcomm             =  100

;        Output control
nstenergy           =  100
nstxout             =  100
nstvout             =  0
nstfout             =  0
nstlog              =  1000
nstxtcout          =  1000

;        Neighbor searching
nstlist             =  10
ns_type             =  grid

;        Electrostatics/VdW
;;;;coulombtype         =  PME
vdw-type            =  Shift
rcoulomb-switch     =  0
rvdw-switch         =  0.9 ;0

;        Cut-offs
rlist               =  1.1
rcoulomb            =  1.1 ;1.0
rvdw                =  1.0

;        Temperature coupling
Tcoupl              =  v-rescale
tc-grps             =  System
tau_t               =  0.1     ;0.1
ref_t               =  400     ;300


;        Velocity generation
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529

;        Bonds
constraints             = all-bonds
constraint-algorithm = lincs

;         Free energy control stuff
free_energy          =   yes
init_lambda          =   0
delta_lambda         =   0
sc_alpha             =   0.5
sc-power             =   1
sc_sigma             =   0.3
couple-lambda0       =   vdw
couple-lambda1       =   none
couple-intramol      =   no

***************************************
Thank you in advance.
Moeed
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