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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