Dear All, I got this problem recently. I want to use g_dist to calculate the distance between two group in my simulation system. However, when I use the implicit solvent for simulation, g_dist went into this problem: Molecule in topology has atom numbers below and above natoms.
I have used tpbconv to create a new tpr file, and also used gmxcheck to check my traj file, they are all consistent. Also, I have never run into this problem when I was using explicit solvent. Hence, I highly suspect this problem comes from the implicit solvent. Really appreciate that you can help me go through this. Thanks a lot! Cheers, Tony :-) g_dist (-: Option Filename Type Description ------------------------------------------------------------ -f traj.trr Input Trajectory: xtc trr trj gro g96 pdb cpt -s nowater.tpr Input Run input file: tpr tpb tpa -n index.ndx Input, Opt! Index file -o dist.xvg Output, Opt. xvgr/xmgr file -lt lifetime.xvg Output, Opt. xvgr/xmgr file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -nice int 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -dist real 0 Print all atoms in group 2 closer than dist to the center of mass of group 1 Reading file nowater.tpr, VERSION 4.5.5 (single precision) Group 0 ( System) has 10199 elements Group 1 ( Other) has 4372 elements Group 2 ( GRA) has 3936 elements Group 3 ( ORA) has 223 elements Group 4 ( HRA) has 213 elements Group 5 ( Protein) has 5827 elements Group 6 ( Protein-H) has 2933 elements Group 7 ( C-alpha) has 375 elements Group 8 ( Backbone) has 1125 elements Group 9 ( MainChain) has 1501 elements Group 10 ( MainChain+Cb) has 1848 elements Group 11 ( MainChain+H) has 1859 elements Group 12 ( SideChain) has 3968 elements Group 13 ( SideChain-H) has 1432 elements Group 14 ( Prot-Masses) has 5827 elements Group 15 ( non-Protein) has 4372 elements Select a group: 1 Selected 1: 'Other' Select a group: 14 Selected 14: 'Prot-Masses' trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Back Off! I just backed up dist.xvg to ./#dist.xvg.1# ------------------------------------------------------- Program g_dist, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/mshift.c, line: 102 Fatal error: Molecule in topology has atom numbers below and above natoms (10198). You are probably trying to use a trajectory which does not match the first 10198 atoms of the run input file. You can make a matching run input file with tpbconv. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "There's No Room For the Weak" (Joy Division) -- 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