Dear Gromacs-users, I have been putting a protein and its hydration shell into the center of an octahedral box and then been filling the remaining space with water using genbox. I wanted to minimise the filled-in water, afterwards, keeping the positions of the protein and the hydration shell fixed with freezegrps.
Performing the minimisation for several conformations of the protein and its hydration shell one minimisation ended with the error message: t = 0.036 ps: Water molecule starting at atom 19012 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates In the minimisation of another conformation I received the error message: Program mdrun, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error:[...] Variable ci has value -2147483648. It should have been within [ 0 .. 294 ] Please report this to the mailing list (gmx-users@gromacs.org) I have chosen the following parameters for constraints and electrostratics: ; OPTIONS FOR BONDS constraints = hbonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration unconstrained-start = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 1e-04 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs-iter = 4 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 30 ; Convert harmonic bonds to morse potentials morse = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 ; Relative dielectric constant for the medium and the reaction field epsilon_r = 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no Does anyone know what went wrong? Thanks Luther _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php