Hi There, I was trying to run a free energy tutorial given at "* http://www.dillgroup.ucsf.edu/group/wiki/index.php?title=Free_Energy:_Tutorial *" While trying the very first run i.e. mdrun using "*min_lbfgs0.mdp*" I ended up with following error ------------------------ ERROR: With coulombtype = PME, rcoulomb must be equal to rlist calling cpp... -------------------------
which i know is valid while using PME for coulombic calculation, but when i tried making rlist=rcoulomb, I got a warning as -------------------------- WARNING 1 [file min_lbfgs0.mdp, line unknown]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb/rvdw. ----------------------------- following is the content of *min_lbfgs0.mdp -------------------------**min_lbfgs0.mdp--------------------- * ; RUN CONTROL PARAMETERS = integrator = l-bfgs nsteps = 5000 ; Output frequency for energies to log file and energy file = nstlog = 1 nstenergy = 1 ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol = 100 emstep = 0.01 ; Max number of iterations in relax_shells = niter = 20 ; Number of correction steps to use for L-BFGS minimization nbfgscorr = 10 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 1 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist = 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r = 1 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths = rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 sc_alpha =0.5 sc-power =1.0 sc-sigma = 0.3 -------------------------------------- Can anybody suggest whether the mdp file has some error or I can use the one with the warning. Thanks in advance, Vivek
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