On 2012-01-06 05:40:24PM +0000, Anna Duncan wrote: > > In my analysis, I want to look at the minimum distance between each > lipid 'atom' and the protein and, for each timepoint, record the > residue or 'atom' in the protein that the lipid 'atom' is closest to. > I can find the minimum distance using g_mindist but there is no option > to record which residue or 'atom' in the protein the lipid 'atom' is > closest to.
g_mindist -o atm-pair.out will give you atom min distance pairs within -d cutoff over the length of the trajectory. > > I've written my own scripts to look at minimum distances and record > the closest-protein-residue information, but where the minimum > distance is between the protein and the lipid atom's periodic image - > when the protein is getting to 'the edge of the box' - these seem to > be really slow running. > > So the question is, is there a quick fix to get g_mindist to record > the information I want it to (or even is there some other blindingly > obvious function + special options that I've missed that will do the > job)? The other solution would be to edit the trajectory so that the > protein always stays in the centre of the box. I have already altered > the trajectory, using g_traj and -pbc nojump (to remove jumps in the z- > direction) then -pbc mol (to remove drift of lipids in the xy-plane), > but I haven't managed to find anything that will maintain the protein > in the box centre throughout the simulation. > > Does anyone have any ideas? Please let me know if, as is usually the > case, I've left out an important bit of information. -center and pick the protein c-alpha as the centering group -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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
