Dear Gromacs Users, I'm using "trjorder" with the following options:
$ trjorder -f systemWithSolv.xtc -n system.atom.ndx -s system.pdb -r 0.35 -nshell system0.35.nshell.xvg As the first group I select all the atoms of a single TYR residue, which is part of a larger protein. As the second group I select all the solvent atoms (TIP3P). For a radius of 3.5 A I observe in most frames the number 8, the observations range from 0 to even 20. What does this number mean exactly? For TIP3P the OH2-H1 and OH2-H2 distance is approx. 1A and the H1 and H2 distance is approx. 1.6A. This gives a "volume" of 4.2A^3 for TIP3P. A sphere of 3.5A would have a volume of 14.6A^3. As a first order approximation this would suggest for non buried TYR residue about 3 to 4 TIP3P molecules which could fit in this sphere. This differs from the number 8 which trjorder measures. My questions are: 1. What does trajorder count? Does it count the number of solvent atoms or of solvent molecules? 2. How does trajorder count? If trajorder counts the amount of molecules. Is it sufficient that a single atom of the molecules is in the sphere to be included in the counting or must all atoms of the molecule be in the sphere to be included in the counting? Thanks, Henri -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
