Hi Vijaya,
could it be that you mixed something up when making the .edi file?
The tool make_edi reads the total number of atoms from the provided
.tpr file and saves this number with the other ED sampling
information to the .edi file.
The ED sampling module in mdrun then compares the number of atoms
from the .edi file with the .tpr file provided to mdrun - to ensure that the
.edi file was produced for the same MD system.
Carsten
On Jun 29, 2010, at 6:57 PM, vijaya subramanian wrote:
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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