Dear Gromacs Users, I tried to energy minimize my system using the steep integrator. However, it gave the following message.
Steepest Descents: Tolerance (Fmax) = 5.00000e+02 Number of steps = 2000 Step= 0, Dmax= 1.0e-02 nm, Epot= 3.96157e+06 Fmax= 1.00697e+06, atom= 14611 Step= 1, Dmax= 1.0e-02 nm, Epot= 2.99970e+06 Fmax= 4.04778e+05, atom= 18527 Step= 2, Dmax= 1.2e-02 nm, Epot= 1.54766e+06 Fmax= 1.52387e+05, atom= 1005 Step= 3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom= 6994 Step= 4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom= 58902 Step= 5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom= 515 Step= 6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom= 188631 Step= 7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom= 188631 Step= 8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom= 188631 Step= 9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom= 188631 Step= 10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom= 188631 step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. After 2000 steps it says, Steepest Descents did not converge to Fmax < 500 in 2001 steps. Potential Energy = -4.6310655e+06 Maximum force = 6.7453154e+03 on atom 18769 Norm of force = 3.3632809e+01 Simulation ended prematurely, no performance report will be written. my em.mdp file contains following parameters. integrator = steep ; simulation algorithm dt = 0.002 ; time step (ps) nsteps = 2000 ; # steps comm_mode = linear ; c.o.m. motion reset ; ; Energy Minimization emtol = 500 ; converged F lt value (kJ mol-1 nm-1) emstep = 0.01 ; initial step size (nm) ; ; Output Control nstxout = 5 ; write coordinates to .trr nstvout = 5 ; write velocities to .trr nstlog = 5 ; write energies to .log nstenergy = 1 ; write energies to .edr ; ; Neightbour Searching cutoff-scheme = Verlet ; scheme used for generating pair list nstlist = 10 ; update neighbour list ns_type = grid ; neighbour list method pbc = xyz ; periodic boundary conditions rlist = 0.9 ; cut-off for short-range neighbour (nm) ; ; Electrostatics and VdW coulombtype = PME ; type of coulomb interaction rcoulomb = 0.9 ; cut-off distance for coulomb epsilon_r = 1 ; dielectric constant rvdw = 0.9 ; cut-off for vdw fourierspacing = 0.12 ; maximum grid spacing for FFT pme_order = 4 ; interpolation order for PME ewald_rtol = 1e-5 ; relative strength of Ewald-shifted DispCorr = EnerPres ; long range dispersion corrections ; ; Temperature Coupling Tcoupl = no ; type of temperature coupling ; ; Pressure Coupling Pcoupl = no ; type of pressure coupling ; ; Velocity Generation gen_vel = no ; generate initial velocities ; ; Bonds constraints = none ; bond constraint type I used gmx solvate to add water molecules to the system. How could I get rid of bad contacts of water molecules? Appreciate if anyone help me to solve the problem. Thank you. Sincerely, A Guruge -- 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.