Hello, On Tue, Sep 24, 2013 at 8:39 AM, Venkat Reddy <venkat...@gmail.com> wrote:
> I have been using the new tool "gmx gangle". My actual intention is to > calculate the orientation between any two same molecules (say cholesterol) > throughout the trajectory and there are 40 cholesterol molecules. But I > couldn't calculate it. I am getting "0" as output. My command is: > gmx gangle -f traj_noPBC.xtc -s topol.tpr -n -g1 vector -g2 vector -group1 > 'resname CHOL and name R5 R0' -group2 'resname CHOL and name R5 R0' -oav > -oall -oh > In its present form, the tool cannot (easily) do what you want. It only supports calculating either a single angle, or a set of angles between fixed pairs of vectors. In your case, you are requesting the tool to calculate the R5-R0 angle between molecules 1-1, 2-2, and so on. Since for all angles, the input vectors are identical, a zero angle is the expected output. It should not be too difficult to extend the tool to do at least part of what you want, by adding an option to either calculate angles from one vector to a set of vectors (e.g., "resname CHOL and resnr N and name R5 R0' and 'resname CHOL and name R5 R0'), or even to calculate the angles between all pairs of vectors. If you have programming experience and would like to extend the tool, feel free to submit your change to gerrit.gromacs.org; I'm more than happy to review and provide comments. Best regards, Teemu -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
