[gmx-users] error with g_dist

Justin Lemkul jalemkul at vt.edu
Mon Aug 26 22:12:12 CEST 2013

On 8/26/13 4:05 PM, chinnu657 wrote:
> Hello all, I am trying to find the distance between 2 centres of mass using
> g_dist.
> I use the command:  g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n
> index.ndx
> but i get the error:
> Fatal error:
> Molecule in topology has atom numbers below and above natoms (1707).
> You are probably trying to use a trajectory which does not match the first
> 1707 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
> I tried using tpbconv like suggested. But that did not help. I really need
> help on this as my submission deadline is getting closer and this is the
> last simulation I need..

The most likely explanation is that you did not save groups correctly using 
xtc-grps in the .mdp file.  In the absence of a description of what you're 
trying to measure, the contents of the index groups, and the gmxcheck output on 
the .xtc file, there's little anyone can do to help.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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