[gmx-users] Residence time and trjorder

Chandan Choudhury iitdckc at gmail.com
Fri Jul 22 14:36:41 CEST 2011


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 kumar Choudhury
NCL, Pune

On Fri, Jul 22, 2011 at 5:12 PM, Carla Jamous <carlajamous at gmail.com> 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 <qiaobf at gmail.com> 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
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