Here I am posting the solution of the problem that I described in my first post:
gmx rdf -f ../../../../traj_200to500.xtc -s ../../../../step7_4.tpr -o -cn
-rmax 0.8 -excl -ref '(resname DPPS and name
O22) and within 0.3 of name CAL' -sel 'name OH2'
Alfredo
Dear gromacs users,
Hello. I am working on bulk water system simulation. I am trying to
calculate tetrahedral order parameters in gromacs by using "gmx hydorder"
command. Dose anyone know how to process outputs generated by "hydorder"
command? It is in the form of output.xpm file.
Thanks in
Hi,
According to the output for "gmx help pdb2gmx",
"Default termini are ionized (NH3+ and COO-), respectively. ... The
AMBER force fields have unique forms for the terminal residues, and these
are incompatible with the -ter mechanism. You need to prefix your N- or
C-terminal residue names