Dear Xavier, my problem is the following:
I'm trying to figure out if a water molecule is present in a specific area around my protein and if so, which water molecule is that and how long does it stay in that place. As you said, if I google residence time, here's the definition: *Residence time* (also known as *removal time*) is the average amount of time that a particle <http://en.wikipedia.org/wiki/Particle> spends in a particular system. But I don't find a tool to calculate this residence time in gromacs, so I'm trying to find a trick that can give me a pourcentage of the time of my simulation where a certain water molecule stays in the specific area of my protein. Regards, Carla On Tue, Jul 12, 2011 at 5:51 PM, XAvier Periole <[email protected]> wrote: > > Dear Boafu, > > This sounds like a great tool! > > Carla, note that once you've ordered the water molecules you loose > the continuity of their trajectories ... that is because you order them in > function of their distance to the protein. > > I am not sure the definition you give will give you the answer to the > residence time. you can google residence time and proteins and see > what come out :)) > > XAvier. > > > On Jul 12, 2011, at 6:32 AM, Baofu Qiao 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 >>> >> >> <g_residence.c>-- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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