Dear Gromacs users I am running a free energy calculation, my simulation crashes and generates different PDB structures I have well equilibrated the system before going to the production and the system seems stable. My input file for production run is as below:- ; Run control integrator = sd ; stochastic leap-frog integrator dt = 0.002 nsteps = 1500000 ; 3 ns comm-mode = Linear ; remove center of mass translation nstcomm = 100 ; frequency for center of mass motion removal
; Output control nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxout-compressed = 5000 ; Bond parameters continuation = yes ; formerly known as 'unconstrained-start' - useful for exact continuations and reruns constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds to H are constrained lincs_iter = 1 ; accuracy of LINCS ; Neighborsearching and short-range nonbonded interactions cutoff-scheme = verlet nstlist = 20 ns_type = grid rlist = 1.2 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Electrostatics coulombtype = PME rcoulomb = 1.2 pme-order = 4 ; interpolation order for PME (default is 4) fourierspacing = 0.16 ; grid spacing for FFT ewald-rtol = 1e-6 ; relative strength of the Ewald-shifted direct potential at rcoulomb ewald_geometry = 3d ; Ewald sum is performed in all three dimensions ; van der Waals vdwtype = cutoff vdw-modifier = Potential-shift-Verlet verlet-buffer-tolerance = 2.5e-04 rvdw = 1.2 DispCorr = EnerPres ; apply long range dispersion corrections for Energy and Pressure ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tc-grps = system ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 298.15 ; Pressure coupling is on for NPT Pcoupl = Parrinello-Rahman pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant (ps) ref_p = 1.0 ; reference pressure (bar) compressibility = 4.5e-05 ; isothermal compressibility of water (bar^-1) ; velocities gen_vel = no ; Velocity generation is on (if gen_vel is 'yes', continuation should be 'no') gen_seed = -1 ; Use random seed gen_temp = 298.15 ; Free energy control stuff free_energy = yes init_lambda_state = 10 delta_lambda = 0 calc_lambda_neighbors = 1 ; only immediate neighboring windows ; Vectors of lambda specified here ; Each combination is an index that is retrieved from init_lambda_state for each simulation vdw_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 coul_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 restraint_lambdas = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ; Options for the decoupling sc-alpha = 0.5 sc-coul = no ; linear interpolation of Coulomb (none in this case) sc-power = 1 sc-sigma = 0.3 nstdhdl = 100 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 Any help would really be appreciated. Thanks. Sadaf -- 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.
