[gmx-users] How to calculate tetrahedral order parameter?

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

[gmx-users] Handling terminal amino acids for Amber

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

Re: [gmx-users] can dynamic selection be used with gmx rdf?

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