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 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.peri...@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>--
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
