Hello Justin<br><br>Thanks for your attention. Just to remind you: I am getting blank dgdl and I found this in log file:<br clear="all"><br>
> There are 0 atoms and 0 charges for free energy perturbation<br><br><br>====================================<br>EM<br>
><br>
> grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr >&<br>
> output.grompp_em<br>
><br>
> mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g em-l0.log -e em-l0.edr<br>
> -v >& output.mdrun_em<br>
><br>
> MD<br>
><br>
> grompp -f md-l0.mdp -c em-l0.gro -p PE60-0c-itp.top -o md-l0.tpr -n<br>
> PE-HEX.ndx>& output.grompp_md<br>
><br>
> mdrun -s md-l0.tpr -o md-l0.trr -c md-l0.gro -g md-l0.log -e md-l0.edr<br>
> -x md-l0.xtc -dgdl md-l0.dgdl -v >& output.mdrun_md<br>================================<br>with mdp :<br><br><br>pbc = xyz <br>energygrps = PE HEX<br> <br>; Run control<br>
integrator = md <br>dt = 0.002 <br>nsteps = 500000 ;5000 <br>nstcomm = 100 <br><br>; Output control<br>nstenergy = 100 <br>
nstxout = 100 <br>nstvout = 0<br>nstfout = 0<br>nstlog = 1000 <br>nstxtcout = 1000 <br><br>; Neighbor searching<br>
nstlist = 10 <br>ns_type = grid <br><br>; Electrostatics/VdW <br>;;;;coulombtype = PME <br>vdw-type = Shift <br>
rcoulomb-switch = 0 <br>rvdw-switch = 0.9 ;0 <br><br>; Cut-offs<br>rlist = 1.1 <br>rcoulomb = 1.1 ;1.0 <br>rvdw = 1.0 <br>
<br>; Temperature coupling <br>Tcoupl = v-rescale <br>tc-grps = System <br>tau_t = 0.1 ;0.1 <br>ref_t = 400 ;300 <br>
<br><br>; Velocity generation <br>gen_vel = yes <br>gen_temp = 300.0 <br>gen_seed = 173529 <br><br>; Bonds<br>constraints = all-bonds <br>
constraint-algorithm = lincs<br><br>; Free energy control stuff<br>free_energy = yes<br>init_lambda = 0 <br>delta_lambda = 0<br>sc_alpha = 0.5<br>sc-power = 1<br>
sc_sigma = 0.3<br>couple-lambda0 = vdw<br>couple-lambda1 = none<br>couple-intramol = no<br><br>***************************************<br>Thank you in advance.<br>Moeed<br>