[gmx-users] g_covar

Dongsheng Zhang dong at pampas.chem.purdue.edu
Tue Feb 28 15:35:48 CET 2006

Hello, everyone,

I have finished a MD simulation of a short peptide. The initial
conformaton of my peptide is the extended conformation, soon the peptide
changed to be a helix and kept it for a long time. I would like to use
g_covar to analyze my simulation with a helix conformation as my
reference structure. I used hyperChem to build the same peptide with a
helix conformation, then I made referrence.tpr. When I uses:
g_covar -f ../full -s reference.tpr -mwa -ref

I got the following error message:
Program g_covar, VERSION 3.3
Source code file: nrjac.c, line: 129

Fatal error:
Error: Too many iterations in routine JACOBI

Could someone tell me where I made a mistake and how to fix it? Thank
you in advance!

More information: all atoms'names and their sequence in reference.tpr
are the same as ../full.xtc except water molecules.


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