[gmx-users] Extracting trajectory

[Jorden Cabal]

Hi Anupama,

I understand your question. But I wonder why do you want all the explicit
water molecules within 5 Angstrom of your protein surface? That would be
meaningless until and unless you are intending to find the conserved water
molecules near the surface of protein. I don't understand your purpose, but
trjcat can not dynamically change the selection automatically at each frame
so directly it is not possible.

Instead you can get the trajectory in appropriate format by using the
"mindist" command which is used for calculating the contacts between two
groups.
Please see the options available with this command, you will find  "-ox"
option which will give you the required trajectory.

For example let's say,
original trajectory=traj.xtc
tpr=run.tpr
Index=index.ndx (group 1 for protein and 13 for sol)

the the command should look like this:
*gmx mindist -f traj.xtc -s run.tpr -n index.ndx -o output.out -n
output.xvg -ox required_traj.xtc -d 0.5 -group*

After being asked you will have to select appropriate group like 1 and 13
for protein and sol from the index file. The output file required_traj.xtc
will contain all the water molecules within 5 Angstrom of protein.
*Important Notes: *
       1: Since there are large number of water molecules in the system,
the calculation time will be very very high. I have not estimated so can
not comment on this  but I am sure that it will take a long.
       2: You will not be able to visualize the .xtc file directly using
visualization package like vmd as they require corresponding .gro file. But
in this case the index of the water molecules will change per frame so its
not             possible. Instead you can directly write in the gro/pdb
formats.

*Although, I do not understand the purpose of your question, I still
suggest you to make intelligent choice of identifying water molecules near
to some interesting cavity instead of whole surface. This will save your
computational time. You can see the following paper for your reference.*

https://www.tandfonline.com/doi/abs/10.1080/1062936X.2018.1537301?journalCode=gsar20


I hope this will solve your problem.
Thank you

Jorden

On Wed, Oct 2, 2019 at 10:32 PM anupama sharma <anusharma.jan1995 at gmail.com>
wrote:

> Dear users,
> I want to extract the trajectory of water molecules near the protein
> surface within 5 angstorm region. I was able to do that in using gmx select
> and gmx trjcat, but it is for only one time frame and than the water
> molecules diffuses away for the next time frame. I want to extract the
> trajectory of only those water molecules that are near protein surface
> within 5 angstorm region for each individual time frame so that i can get
> the complete trajectory of water molecules that are near the protein
> surface excluding the water molecules that diffuses away in each next
> frame......
> I will be thankful for help.
>
>
>
>
> Thanks and regards,
> Anupama
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