| VERSION 4.0 |
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./configure make make install |
./configure --enable-float make make install |
make distclean ./configure make make install |
CPPFLAGS="-I/home/erik/fftw/include" |
LDFLAGS="-L/home/erik/fftw/lib" |
setenv CPPFLAGS "-I/path/to/your/mpi/include" setenv LDFLAGS "-L/path/to/your/mpi/lib" setenv LIBS "-lmpi" setenv MPICC "cc" |
setenv LD_LIBRARY_PATH "$LD_LIBRARY_PATH:/opt/lib" |
trjcat -o whole.trr part1.trr part2.trr part3.trr |
eneconv -o whole.edr part1.edr part2.edr part3.edr |
pdb2gmx -f eiwit.pdb -reth -ter -n |
The next step is:
trjconv -f eiwit.pdb -o eiwit.xtc -n clean -timestep 1 -box 10 -center |
A not very exiting but mandatory step is:
grompp -f grompp.mdp -c conf.gro -p topol.top |
Now, suppose you want to calculate all cross-rmsd values for all
structures. Enter:
g_rms -f eiwit.xtc -s topol.tpr -m |
Of course there are many more analysis tools available. For example ngmx a trajectory viewer. A list of all tools is available in the online manual.
g_confrms -f1 file1.xxx -f2 file2.xxx |