[gmx-users] g_dist problem in Implicit solvent

[Justin Lemkul]

On 5/14/13 7:26 PM, Tong Li wrote:
> 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.
>

So, just to clarify, did you run an implicit solvent simulation, or did you 
simply remove the water from your .tpr file to do analysis and post-processing? 
  The latter is particularly error-prone and can be the source of your problem. 
  I have never had issues in using analysis tools with true implicit solvent 
simulations.

In any case, gmxcheck should be useful in telling you about the contents of the 
index groups.  Just because there are the "right" number of atoms in the system, 
does not mean that the atom numbers are necessarily within that number if you 
stripped other coordinates out.

-Justin

> 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)
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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