Hi
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.
Thanks
Vijaya
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