Hello gromacs users, I want to analyze a liquid interface by producing a series of histograms that profile different slices of my simulation along the cartesian z axis. In each histogram, I want to bin the angles between the z-axis and the normal vector defined by a plane of three atoms in a flat molecular ring. I have many of these rings in my simulation.
I downloaded the development version of gromacs and read the documentation associated with g_select and gmx gangle. As I understand it, my index file should select the atoms that define each normal vector. To properly profile a slice, the selection should be dynamic. Atoms *defining the plane* that drift into a slice during a simulation must be selected. Atoms *defining the plane* that drift out of a slice must be deselected. Also, it would be nice to make this spatial dynamic selection based on the center of geometry of the *atoms that define the plane* or some other sensible molecular substructure. My index file looks something like this... [ a_plane ] 1 2 3 10 11 12 ... ...where each row lists that ring atoms that define the plane in exactly the same way. Assuming I define a given slice to be between 0 and 1 on the z axis, I believe the command that will produce what I want is: gmx gangle -f file.trr -s file.tpr -n file.ndx -g1 plane -group1 'z 0 to 1 and group a_plane' -g2 z -oh file.xvg -binw 1.0 A few questions/comments: 1.) I am unsure how I should set the '-selrpos' option. The gangle program requires all three atoms to compute the angle so I suspect that the prefix 'whole_' is necessary. What is the difference between the "res_" and "mol_" infix? I was hoping the index file would restrict the computation of the reference position so that 'whole_res_cog' would work but it seems to compute the cog for the whole residue, not that atoms that define the plane. For clarity, if the cog of the three atoms that define the plane lie within the slice, I want all three atoms that define the plane to be selected. 2.) Is it possible to use a custom set of atoms for computation of the cog that differs from the atoms I want selected if this cog is within the slice? For example, consider benzene. The program gangle requires three benzene atoms to define a plane but the cog of these atoms is not the cog of the ring. I suspect this is not possible with the gromacs tools. 2.) It seems the flag '-oall' outputs the angles for all the normal vectors defined by the atoms in my index file. Is this want most users will want from this tool? If I have selection like 'z 0 to 1 and group a_plane', it makes more sense for '-oall' to print all the selected angles, correct? Best, Eric -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
