For Linux:

export SD=~/workspace/soft
mkdir -p $SD

cd $SD

tar xzf tcl8.5.18-src.tar.gz
cd tcl8.5.18/unix/
./configure --prefix=$SD/tcl --enable-treads
make
make install

cd $SD

tar xzf netcdf-c-4.3.3.1.tar.gz 
cd netcdf-c-4.3.3.1/
./configure --prefix=$SD/netcdf --disable-netcdf-4 --disable-dap
make check install

cd $SD

tar xzf vmd-1.9.1.src.tar.gz
mv plugins/ vmd-1.9.1/plugins/
cd vmd-1.9.1/plugins/

export PLUGINDIR=$SD/vmd/plugins

make LINUXAMD64 TCLINC=-I$SD/tcl/include/ TCLLIB=-L$SD/tcl/lib NETCDFINC=-I$SD/netcdf/include NETCDFLIB=-L$SD/netcdf/lib
make distrib

ln -s $PLUGINDIR/LINUXAMD64 .
cd ../

export VMDINSTALLLIBRARYDIR=$HOME/workspace/soft/vmd
export VMDINSTALLBINDIR=$HOME/workspace/soft/vmd/bin

cd lib/
ln -s $SD/netcdf netcdf
cd netcdf
ln -s lib/ lib_LINUXAMD64
cd ../../

export TCL_LIBRARY_DIR=$HOME/workspace/soft/tcl/lib
export TCL_INCLUDE_DIR=$HOME/workspace/soft/tcl/include
./configure LINUXAMD64 IMD SILENT TCL PTHREADS NETCDF
cd src/
make clean
make
make install

echo "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$SD/netcdf/lib" >> ~/.bashrc
echo "alias vmd=$SD/vmd/bin/vmd" >> ~/.bashrc 
echo "alias catdcd=$SD/vmd/plugins/LINUXAMD64/bin/catdcd4.0/catdcd" >> ~/.bashrc