Dear Tsjerk Thanks for your consideration.
My system contains 2 components: (DOPC & cholesterol) lipids + water molecules. I get force field parameters from lipid book (for dopc and cholesterol). I used input coordinate file (system.gro) from following web site: http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html em.mdp file is as follows: ------------------------------------------------------------------------------------- ; em.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 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 ----------------------------------------------------------------------------------------- For doing minimization, I used following command: grompp -f em.mdp -c system.gro -p topol.top -o em.tpr and then I get following result: ------------------------------------------------------------------------------------- WARNING 1 [file topol.top, line 32]: 3632 non-matching atom names atom names from topol.top will be used atom names from system.gro will be ignored Analysing residue names: Warning: file does not end with a newline, last line: IB+ Ion There are: 128 Other residues There are: 1706 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 29019.00 Largest charge group radii for Van der Waals: 1.541, 1.514 nm Largest charge group radii for Coulomb: 0.079, 0.079 nm WARNING 2 [file em.mdp]: The sum of the two largest charge group radii (3.054313) is larger than rlist (1.200000) Calculating fourier grid dimensions for X Y Z Using a fourier grid of 72x72x72, spacing 0.111 0.120 0.116 Estimate for the relative computational load of the PME mesh part: 0.62 NOTE 1 [file em.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This run will generate roughly 133 Mb of data There was 1 note There were 2 warnings ------------------------------------------------------------------------------------- I used -maxwarn option and I obtained em.tpr file. Then, for doing minimization, I used following command: mdrun -s em.tpr -o em.trr -c em.gro -e em.edr -g em.log and then I get following result: ------------------------------------------------------------------------------------- Reading file em.tpr, VERSION 4.5.1 (single precision) Starting 4 threads Making 2D domain decomposition 1 x 2 x 2 Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 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 881 steps, but did not reach the requested Fmax < 1000. Potential Energy = 2.1828770e+05 Maximum force = 1.3656898e+04 on atom 618 Norm of force = 5.1748779e+02 ------------------------------------------------------------------------------------- When I see created gro file (em.gro) by VMD, some dopc or cholesterol molecules are broken to 2 or 3 parts. I tested different ways: 1) change of parameters in em.mdp file ( emstep, nstep, EM algorithm ) 2) change of box size 3) I used the newest version of gromacs (4.6.3) But, unfortunatele, my problem was not solved. Certainly, I can not use this structure for next step (equilibration). How to solve this problem. Any help will highly appreciated. Best wishes for you -- 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
