[gmx-users] Problem with 4.0.3

[David van der Spoel]

Stephen P. Molnar wrote:
> I have just downloaded and installed 4.0.3.  I received neither warning 
> nor error during the process.  However when I attempt to run the gmxdemo 
> I get:
> 
> Fatal error:
> Library file F.dat not found in current dir nor in default directories
> 
> each successive step in demo gets a corresponding error message.  Yet 
> the 'missing' files, e.g. FF.dat are in 
> /sdb5/Applications/gromacs/share/gromacs/top
> 
> Here is what I put in my .bashrc file:
> 
> ##########################################################
> # This is the real configuration part. We save the Gromacs
> # things in separate vars, so we can remove them later.
> # If you move gromacs, change the next four line.
> ##########################################################
> GMXBIN=/sdb5/Applications/gromacs/bin
> GMXLDLIB=/sdb5/Applications/gromacs/lib
> GMXMAN=/sdb5/Applications/gromacs/share/man
> GMXDATA=/sdb5/Applications/gromacs/share
>   # NB: The variables already begin with ':' now, or are empty
> LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH}
> PATH=${GMXBIN}${PATH}
> MANPATH=${GMXMAN}${MANPATH}

Try:

. /sdb5/Applications/gromacs/bin/GMXRC


> 
> # export should be separate, so /bin/sh understands it
> export GMXBIN GMXLDLIB GMXMAN GMXDATA LD_LIBRARY_PATH PATH MANPATH
> 
> Obviously I've installed gromacs in a non-default location.  What 
> modifications should I make, I presume to .cashrc, so that the necessary 
> files will be found?
> 
> Thanks in advance.
> 
> -- 
> Stephen P. Molnar, Ph.D.        Life is a fuzzy set
> Foundation for Chemistry        Stochastic and multivariate
> http://www.geocities.com/FoundationForChemistry
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se