Dear users I tried energy minimization of POPE/POPG bilayer from http://www.softsimu.net/downloads/pepg-mix.pdb . Process stopped and forces have not converged to requested precision (output shown below). I used Gromacs version 2019.2 .
My colleague also used this bilayer before with earlier version of Gromacs (don't know which one, sorry, few years ago), and everything works fine. I tried a few different bilayers constructed from this one, and noticed that different atoms causes a problem (Fmax on it) but each time it's about H6 atom in some DPO molecule. I checked, and there is no steric clashes with periodic images or solution molecules. Any suggestions what could be wrong? Thanks Below are tipical gromacs output and mdp file: ********* Gromacs output: Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 Step= 0, Dmax= 1.0e-02 nm, Epot= -3.45240e+05 Fmax= 6.29238e+03, atom= 5580 Step= 1, Dmax= 1.0e-02 nm, Epot= -3.51348e+05 Fmax= 3.62527e+03, atom= 1772 Step= 2, Dmax= 1.2e-02 nm, Epot= -3.55043e+05 Fmax= 1.07906e+04, atom= 1772 Step= 3, Dmax= 1.4e-02 nm, Epot= -3.58399e+05 Fmax= 6.04668e+03, atom= 524 Step= 4, Dmax= 1.7e-02 nm, Epot= -3.58764e+05 Fmax= 1.66084e+04, atom= 524 Step= 5, Dmax= 2.1e-02 nm, Epot= -3.62991e+05 Fmax= 3.55133e+04, atom= 6325 Step= 6, Dmax= 2.5e-02 nm, Epot= -3.66326e+05 Fmax= 3.14946e+05, atom= 6325 Step= 7, Dmax= 3.0e-02 nm, Epot= -3.66358e+05 Fmax= 6.27472e+04, atom= 6005 Step= 8, Dmax= 3.6e-02 nm, Epot= -3.70907e+05 Fmax= 7.76457e+05, atom= 6217 Step= 10, Dmax= 2.1e-02 nm, Epot= -3.71321e+05 Fmax= 1.24828e+06, atom= 5581 Step= 14, Dmax= 3.2e-03 nm, Epot= -4.38973e+05 Fmax= 7.26301e+07, atom= 5583 Step= 18, Dmax= 4.8e-04 nm, Epot= -4.39005e+05 Fmax= 1.17286e+08, atom= 5581 Step= 28, Dmax= 1.1e-06 nm, Epot= -4.39005e+05 Fmax= 1.16818e+08, atom= 5581 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. *************** minim.mdp: integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 50000 nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 pbc = xyz ***************** -- 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.