Dear Justin Very thanks for your reply.
You said "I suspect your Gromacs version is somewhat outdated, as recent versions account for periodicity when making this check". I used 4.5.5 version of gromacs. What version of gromacs is more appropriate for my case. Based on your suggestion, I used -maxwarn option for grompp. Then I used -nt 1 option for mdrun, but this step takes too long and Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 Warning: 1-4 interaction between 434 and 407 at distance 3.023 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation ******************** This usually means your system is exploding, ******************** if not, you should increase table-extension in your mdp file or with user tables increase the table size step 23: Water molecule starting at atom 10613 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates 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. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 2122 steps, but did not reach the requested Fmax < 1000. Potential Energy = 1.4310875e+05 Maximum force = 2.7179752e+04 on atom 5271 Norm of force = 4.0253470e+02 -------------------------------------------------------------------------------------- my em.mdp file is as follows: 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 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 ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; Short-range electrostatic cut-off rvdw = 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions -------------------------------------------------------------------------------------- gro, edr, trr and lof file were created. I increased emstep from 0.01 to 0.1 and I used constraints = none in mdp file, but result are the same. Is this minimization completely true? Can I use created gro file of this minimization for next step (equilibration)? I am beginner in gromacs, please help me to resolve this problem. Best wishes -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
