[gmx-users] g_dist problem in Implicit solvent

Tong Li t14.li at qut.edu.au
Wed May 15 01:26:48 CEST 2013

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!


                                :-)  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)

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