Carla, The g_residence.c is written in accord to gmx-4.5.4 format. What you can do is copy it to the src/tools directory. Make a subsequent changes in the Makefile present there and the do make to compile. This will generate g_residence executable, which can be used.
But I did not understand, how the output trajectory of trjorder can be used for the analysis of the residence time of a water molecule i.e; the number of times a particular water molecule constantly stays in a radius of 5 A. Guidance is always welcome. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Jul 22, 2011 at 5:12 PM, Carla Jamous <[email protected]> wrote: > > 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 > -- 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
