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". -- View this message in context: http://gromacs.5086.n6.nabble.com/TMD-using-free-energy-code-tp5006260p5006321.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
