[gmx-users] Residence time and trjorder

Chandan Choudhury iitdckc at gmail.com
Thu Jul 14 09:25:56 CEST 2011


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 <x.periole at rug.nl> 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 <x.periole at rug.nl> 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>--
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