hi It seems that your couple-moltype is missing, that is, no molecules will be turned off interaction.
dawei On Thu, Feb 17, 2011 at 8:26 AM, Moeed <[email protected]> wrote: > 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 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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