[gmx-users] Residence time and trjorder

Carla Jamous carlajamous at gmail.com
Fri Jul 22 13:42:23 CEST 2011

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,

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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