Dear all, I am doing the free energy calculation using Gromacs 4.6.4 now. However, I got the message by g_bar: ----------- Program g_bar, VERSION 4.6.4 Source code file: /home/rui/Downloads/gromacs-4.6.4/src/tools/gmx_bar.c, line: 1208
Fatal error: Could not find a set for foreign lambda = 0.000000 in the files for lambda = 0.000000 --------- Could anyone help me to resolve this problem. Please also see my mdp input: --------------------------- ; Run control integrator = sd ; Parameters describing what to do, when to stop and what to save nsteps = 5000000 ; Maximum number of (minimization) steps to perform 12000ns dt = 0.002 ; 2fs ; Output control cutoff-scheme = group nstlog = 100 nstenergy = 10 nstcalcenergy = 10 ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ns_type = grid pbc = xyz rlist = 1.2 ; Electrostatics coulombtype = PME rcoulomb = 1.2 ; van der Waals vdw-type = cut-off ;rvdw-switch = 0.9 rvdw = 1.2 ;vdw-modifier=Potential-shift-Verlet ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ;Temperature coupling tcoupl=V-rescale ;berendsen tc_grps=Protein CA2+_Water_and_ions tau_t=0.1 0.1;ps time constant for coupling for each group ref_t=300 300;K reference temperature ; Pressure coupling pcoupl = Parrinello-Rahman Pcoupltype=isotropic tau_p=0.5 ref_p=1.0 compressibility=4.5e-5 refcoord_scaling=com ; Free energy control stuff free_energy = yes init_lambda = 0.1 init-lambda-state = -1 delta_lambda = 0 fep-lambdas = 0 0.2 ;coul-laambdas couple-intramol = yes sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 nstdhdl = 10 ; Generate velocities to start gen_vel = no ; Type of constraint algorithm constraints = h-bonds constraint-algorithm = lincs continuation = yes ld_seed =-1 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 ; Output control nstxout = 1000 ; frequency to write coordinates to output trajectory file ;energygrps = Protein; Which energy group(s) to write to disk ------------ Thank you very much for any help! Sincerely, Rui Zhang -- Dr. Rui Zhang Postdoctoral Research Associate Department of Veterinary Pathobiology Texas A&M University College Station, TX 77840 [email protected] (305) 301-7879 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
