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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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