Dear Users, I’m performing relative binding free energy by using Gromacs 5.0.5. As I understood reading the sections 5.3.4, 6.1 and 7.3.23 of the GROMACS 5.0.5 manual I should avoid to use couple-moltype and couple-lambda0/couple-lambda1 because they would override the A and B states, already defined in the topology file. For this reason I put couple-lambda0 = none, couple-lambda1 = none and couple-intramol = yes to specify I want to modify intramolecular interactions. The problem I’m having regards the couple-moltype. If I don’t use it in the mdp file the minimization crashes and if I try to use couple-moltype=none I have the error ‘no such a molecule named none’ (as expected because this parameter is referred to the [moleculetype] section). Could someone that has more experience in this field than me give a look to my mdp file and help me to solve this problem, please. Thank you! NB the following mdp file is an example of my minimization mdp files for lambda=0
; RUN CONTROL PARAMETERS integrator = steep ; Start time and timestep in ps tinit = 0 dt = 0.002 nsteps = 2500 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 100 ; must be equal or larger than calcenergy nstcalcenergy = 100 ; Default ; CUTOFF SCHEME (default = verlet now) cutoff-scheme = group ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 100 emstep = 0.01 ; Max number of iterations in relax_shells niter = 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr = 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Checkpointing helps you continue after crashes, they are always included now ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy = 100 ; Output frequency and precision for xtc file nstxout-compressed = 0 compressed-x-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme rcoulomb-switch = 0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field ; Method for doing Van der Waals vdw-type = Cut-off vdw-modifier = Potential-switch ; cut-off lengths rvdw-switch = 0.9 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = AllEnerPres ; Extension of the potential lookup tables beyond the cut-off ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.10 ; 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 ewald_geometry = 3d epsilon_surface = 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = no ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 2.0 ref_t = 298.15 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1 compressibility = 4.5e-5 ref_p = 1.01325 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 298.15 gen_seed = 1993 ; OPTIONS FOR BONDS constraints = hbonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration continuation = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 1e-04 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 30 ; Convert harmonic bonds to morse potentials morse = no ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are excluded energygrp_excl = ; Free energy control stuff free-energy = yes init_lambda_state = 0 fep_lambdas = 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 vdw_lambdas = 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 ;couple-moltype = LIG couple-lambda0 = none couple-lambda1 = none couple-intramol = yes sc-alpha = 0.5 sc-sigma = 0.3 sc-power = 1.0 sc-r-power = 6 sc-coul = no nstdhdl = 100 calc-lambda-neighbors = -1 — Dr. Stefania Evoli Post-Doctoral Fellow King Abdullah University of Science and Technology Catalysis center - Bldg. 3, 4th floor, 4231–WS18 Thuwal, Kingdom of Saudi Arabia stefania.ev...@kaust.edu.sa ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -- 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 gmx-users-requ...@gromacs.org.