Hi gmx-users, I tried installing the tool, g_residence.c
I am using gromacs-4.0.7 I copied it to the src/tools. There, I executed make command # make g_residence cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -I/opt/fftw-3.2.2/include -L/opt/fftw-3.2.2/lib g_residence.c -o g_residence g_residence.c:42:22: fatal error: sysstuff.h: No such file or directory compilation terminated. make: *** [g_residence] Error 1 How do the tool can be installed? Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Jul 13, 2011 at 8:24 PM, XAvier Periole <[email protected]> wrote: > > Mark is right g_dist can help you for this but there is no specific > tool calculating residence time ... I guess everyone dreams of > someone writing it :)) > > On Jul 13, 2011, at 2:28 AM, Mark Abraham wrote: > > On 13/07/2011 5:52 PM, Carla Jamous wrote: > > 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. > > > I think g_dist does this for a group containing a single water molecule. > All you need to do write a script to iterate over each molecule, and then > collate the statistics. > > Mark > > 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 >>> 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 thewww 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 > > > > -- > 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 >
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