Dear Gromacs users, When I tried to run the equilibration run, it gave several LINCS WARNINGS. However, that equilibration run is completed by the Gromacs. Do I have to concern about these warnings or can I ignore those?
Thank you. Sincerely, A. Guruge On Fri, Oct 20, 2017 at 11:22 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/19/17 8:21 PM, Amali Guruge wrote: > >> 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? >> > > That happens often during minimization, especially the early steps. If it > doesn't come back up again, it's fine. It should never happen during MD. > > -Justin > > > 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 >>> <https://maps.google.com/?q=pped+after+2000+steps+because+you+told+it&entry=gmail&source=g> >>> 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. >>> >>> > -- > ================================================== > > 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? 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