Remove water from xtc file

User discussions
1

GROMACS version: 2020.7
GROMACS modification: No

I want to use Prolint Webserver for peptide/membrane interaction and i need to remove water and ions from the XTC file (required by the webserver).
Do i use gmx trjconv ? How exactly ?

2

You can use gmx trjconv with an index file (-n) containing the molecules you want to output in an index group.

3

oh, i see thank you>
i did gmx trjconv but i strugled to select all at once
Select group for output
Group 0 ( Protein) has 118 elements
Group 1 ( POPC) has 4308 elements
Group 2 ( POPS) has 1068 elements
you got an idea ?

4

Generate a new index file with an index group containing the atoms you want to keep in your file. gmx make_ndx will help you.

5

that is what i did but when i do
gmx trjconv -f file.xtc -n index.ndx
i have
Select group for output
Group 0 ( Protein) has 118 elements
Group 1 ( POPC) has 4308 elements
Group 2 ( POPS) has 1068 elements
and i cant select all of them at once apparently

6

That means that you do not have an index group with all the atoms you want to keep. Use gmx make_ndx to create a new one, i.e. a new group that contains Protein + POPC + POPS.

If you find it difficult to do that using make_ndx then you can do it manually by editing your index file. The format is simple:

[ Protein-POPC-POPS ]
<enter the numbers of all relevant atoms here, e.g. by copying and pasting>
7

Thank you very much
Have a nice day