Hi Baofu, Please can you tell me how to install g_residence.c in gromacs?
If I understood well, the line command is the following: g_residence -s toplogy.tpr -f trajectory.xtc -o output What is the format of the output? Thank you, Carla On Tue, Jul 12, 2011 at 2:32 PM, Baofu Qiao <[email protected]> wrote: > HI Carla, > > I wrote a similar code, see attached. But it is written for my condition. > You should modify it accordingly. > > regards, > Baofu Qiao > > > On 07/12/2011 02:04 PM, Carla Jamous wrote: > >> Dear gmx-users, >> >> I used trjorder in order to study the water molecules that are closer than >> 5 A from my protein. >> >> trjorder -s structure.tpr -f traj.xtc -n prot_water.ndx -o ordered.pdb >> -nshell nshell_.xvg -r 0.5 -b 0 -e 5000 >> >> But now I need to analyse the residence time of a water molecule, I mean >> the number of times a single water molecule stays in a radius of 5 A of the >> protein and divide this number by the total number of conformations, in >> order to have a pourcentage value. >> >> Please is there any gromacs tool able to do this calculation or else does >> anyone have an idea of how to do that? >> >> Thank you >> >> Carla >> > >
-- 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
