Did you look at atom 2073? Catch ya,
Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of liaoxyi Sent: Wednesday, 12 October 2011 3:59 PM To: gmx-users@gromacs.org Subject: [gmx-users] Implicit solvent problems Hi, dear all, I'm doing the simulation involved in protein and some surface. I encounter this problem when trying to use implicit solvent model with GMX4.5.3. First, minimize. When doing this I got the result as below: Step= 0, Dmax= 1.0e-02 nm, Epot= -1.91727e+06 Fmax= 6.19542e+06, atom= 2073 Step= 1, Dmax= 1.0e-02 nm, Epot= -1.99260e+06 Fmax= 1.05712e+06, atom= 2073 Step= 2, Dmax= 1.2e-02 nm, Epot= -2.09734e+06 Fmax= 1.79058e+05, atom= 2073 Step= 4, Dmax= 7.2e-03 nm, Epot= -2.17474e+06 Fmax= 7.22113e+04, atom= 2073 Step= 6, Dmax= 4.3e-03 nm, Epot= -2.17724e+06 Fmax= 4.33926e+04, atom= 2073 Step= 8, Dmax= 2.6e-03 nm, Epot= -2.18069e+06 Fmax= 3.24778e+04, atom= 2073 Step= 10, Dmax= 1.6e-03 nm, Epot= -2.18404e+06 Fmax= 2.76114e+04, atom= 2073 Step= 13, Dmax= 4.7e-04 nm, Epot= -2.18500e+06 Fmax= 2.63803e+04, atom= 2073 Step= 17, Dmax= 7.0e-05 nm, Epot= -2.18514e+06 Fmax= 2.62045e+04, atom= 2073 Step= 19, Dmax= 4.2e-05 nm, Epot= -2.18522e+06 Fmax= 2.61000e+04, atom= 2073 Step= 22, Dmax= 1.3e-05 nm, Epot= -2.18524e+06 Fmax= 2.60689e+04, atom= 2073 Step= 23, Dmax= 1.5e-05 nm, Epot= -2.18527e+06 Fmax= 2.60315e+04, atom= 2073 Step= 27, Dmax= 2.3e-06 nm, Epot= -2.18527e+06 Fmax= 2.60258e+04, atom= 2073 Step= 29, Dmax= 1.4e-06 nm, Epot= -2.18488e+06 Fmax= 2.60222e+04, atom= 2073 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 30 steps, but did not reach the requested Fmax < 1000. Potential Energy = -2.1852700e+06 Maximum force = 2.6025840e+04 on atom 2073 Norm of force = 2.2667976e+03 --------------------------------------- >From above, the force is extremely large. And I don't know why. the minim.mdp is as below: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = Cut-off ; for Implicit solvent long-range electrostatics rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) ; implicit_solvent implicit_solvent = GBSA gb_algorithm = OBC nstgbradii = 1 rgbradii = 1.0 gb_epsilon_solvent = 78.3 gb_obc_alpha = 1 ; OBC(II) gb_obc_beta = 0.8 ; OBC(II) gb_obc_gamma = 4.85 ; OBC(II) gb_dielectric_offset = 0.09 ----------------- Is there any item that's not proper or needed to add? Is the minimization necessary for implicit solvent? Thank you again for your reading. Kiara
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