Dear All, I am interested in simulation of cyclohexane box based on Lemkul tutorial. At first I built a box using following commandgmx insert-molecules -ci chx.gro -nmol 500 -box 2.154434 2.154434 2.154434 -o chx_box.gro (I want a box with 10 nm3 volume)after run several times and convergence I have a box with 88 CHX. then I minimized energy using following mdp file:====================; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 100.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 500000 ; 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 cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1 ; Short-range electrostatic cut-off rvdw = 1 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no)================================================== OOPS!! I got following fatal error ============= GROMACS: gmx grompp, VERSION 5.0.4 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx grompp -f minim.mdp -c chx_box.gro -p chx_box.top -o em.tpr Back Off! I just backed up mdout.mdp to ./#mdout.mdp.41# NOTE 1 [file minim.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 1763529642 Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'chx' Warning: atom name 1 in chx_box.top and chx_box.gro does not match (CAA - AA) Warning: atom name 2 in chx_box.top and chx_box.gro does not match (CAB - AB) Warning: atom name 3 in chx_box.top and chx_box.gro does not match (CAE - AE) Warning: atom name 4 in chx_box.top and chx_box.gro does not match (CAF - AF) Warning: atom name 5 in chx_box.top and chx_box.gro does not match (CAD - AD) Warning: atom name 6 in chx_box.top and chx_box.gro does not match (CAC - AC) Warning: atom name 7 in chx_box.top and chx_box.gro does not match (CAA - AA) Warning: atom name 8 in chx_box.top and chx_box.gro does not match (CAB - AB) Warning: atom name 9 in chx_box.top and chx_box.gro does not match (CAE - AE) Warning: atom name 10 in chx_box.top and chx_box.gro does not match (CAF - AF) Warning: atom name 11 in chx_box.top and chx_box.gro does not match (CAD - AD) Warning: atom name 12 in chx_box.top and chx_box.gro does not match (CAC - AC) Warning: atom name 13 in chx_box.top and chx_box.gro does not match (CAA - AA) Warning: atom name 14 in chx_box.top and chx_box.gro does not match (CAB - AB) Warning: atom name 15 in chx_box.top and chx_box.gro does not match (CAE - AE) Warning: atom name 16 in chx_box.top and chx_box.gro does not match (CAF - AF) Warning: atom name 17 in chx_box.top and chx_box.gro does not match (CAD - AD) Warning: atom name 18 in chx_box.top and chx_box.gro does not match (CAC - AC) Warning: atom name 19 in chx_box.top and chx_box.gro does not match (CAA - AA) Warning: atom name 20 in chx_box.top and chx_box.gro does not match (CAB - AB) (more than 20 non-matching atom names) WARNING 1 [file chx_box.top, line 58]: 528 non-matching atom names atom names from chx_box.top will be used atom names from chx_box.gro will be ignored Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 88 Other 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 1581.00 WARNING 2 [file minim.mdp]: You are using full electrostatics treatment PME for a system without charges. This costs a lot of performance for just processing zeros, consider using Cut-off instead. Calculating fourier grid dimensions for X Y Z Using a fourier grid of 20x20x20, spacing 0.108 0.108 0.108 Estimate for the relative computational load of the PME mesh part: 0.23 This run will generate roughly 2 Mb of data There was 1 note There were 2 warnings ------------------------------------------------------- Program gmx, VERSION 5.0.4 Source code file: /home/mohsen/Downloads/gromacs-5.0.4/src/gromacs/gmxpreprocess/grompp.c, line: 2087 Fatal error: Too many warnings (2), gmx terminated. If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ============================================= any suggestion is appreciated best, Mohsen -- 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.