Dear Gromacs users, Thank you very much for the reply. My concern is "step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate". What should I do to avoid it?
Thank you. On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/19/17 8:10 PM, Amali Guruge wrote: > >> 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. >> > > mdrun stopped after 2000 steps because you told it to. You need to > minimize further, so increase nsteps (or set it to -1 to let mdrun go as > long as it needs to without having to guess a number). > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > 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. > -- 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.