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]
<mailto:[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
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