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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