[gmx-users] ED sampling

vijaya subramanian vijaya65 at hotmail.com
Tue Jun 29 18:57:02 CEST 2010

I need some information about how ED sampling works when 
a subset of the atoms are used for covariance analysis.  Basically I would like to
move the system along the first eigenvector obtained from covariance analysis of the
C-alpha atoms only.  From the paper "Toward an Exhaustive Sampling of the Configurational Spaces of two forms of the Peptide Hormone Guanylin"  it appears only the C-alpha atoms are used  to define
the essential subspace but when I use the following commands, I get an error message saying:

Fatal error:
Nr of atoms in edsamp26-180fit.edi (4128) does not match nr of md atoms (294206)

The commands are:
tpbconv -s full180.tpr -f full180.trr -extend 5 -o edsam26-180f180.tpr -e full180.edr
aprun -n 60 $GROMACS_DIR/bin/mdrun -s edsam26-180f180.tpr -nosum -o edsam26-180f180.trr -x edsam26-180f180.xtc -ei edsamp26-180fit.edi -c edsam26-180f180.gro -e edsam26-180f180.edr -g edsam26-180f180.log

The ED sampling method I am using is  linfix not radacc.


The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. 
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