Hi, On Wed, May 8, 2013 at 4:44 PM, Albert <mailmd2...@gmail.com> wrote:
> I am trying to run g_select with command: > > g_select -f md.xtc -s md.pdb -os water.xvg -sf selection.dat > > in the selection.dat I defined the following: > > watero= name 0 and resname T3P; > close = water0 and within 0.6 of resid 50; > close; > > my residue 50 is in the deep pocket of protein and there is only max. 12 > water near 6A. However, I found that in almost all my trajectories, there > are at least 16 water from the g_select output. I am just wondering, is > there anything wrong of my defenition in selection.dat? > There's nothing obvious wrong with the selections (if you don't count mismatches between the letter O and the number 0, which should give you errors if you really had those in your input). You can try to diagnose the issue with the -oi and/or -on flags for g_select to see what exactly gets selected. You should also ensure that "resid 50" selects the residue you expect and nothing else. If you think that something is getting selected incorrectly, please provide additional information like your Gromacs versions and what exactly is selected and why it shouldn't. 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
