[gmx-users] perl water_deletor.pl

[Salman Zarrini]

Hi
On Fri, Jan 18, 2019 at 3:30 AM rabee khorram <rabeeh.khorram at gmail.com>
wrote:

> *Hello everyone, *
> *I am running liposome structure with gromacs 5.*
> *this liposome created with Packmol software(without water molecules).*
> *after Solvating liposome with water in gromacs, I need to remove waters
> from hydrophobic region.*
>
I guess the gmx select can do the job for you, something like:
~> gmx select -f conf.gro -s conf.tpr -selrpos mol_cog -on water.ndx
> resname SOL and not within 1 of [x0, y0, z0]    % (This is just an
example region; you should define the region of your interest here)
Gives you the water.ndx which contains the index numbers of the water
molecules of your interest.
Then somthing like:
~> gmx trjconv -f conf.gro -s conf.tpr -n water.ndx -o water.gro
Gives you the water molecules of your interest.
For further examples please have a look at "
http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html"

Cheers,
Salman


> *is these  any "perl water_deletor.pl <http://water_deletor.pl> " script
> for this structure?*
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