[gmx-users] ED sampling

Carsten Kutzner ckutzne at gwdg.de
Wed Jun 30 10:11:08 CEST 2010

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.


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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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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