Trjorder command- Help

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question

I cannot to calcule SDF of Na in aqueous solution. As result have a sphere big, I think that must set Na as a reference molecule to fix this issue.
Would anybody know-how set the reference molecule with trjorder command?

2

The reference molecule and the molecules to be reordered are defined in the index file. With the command -n the index file will be read by gmx trjorder. with the option -da you can control how to define the position of the reference
see more https://manual.gromacs.org/2021/onlinehelp/gmx-editconf.html

Best regards
Alessandra

3

Thank you for your reply.
Nonetheless, I’ve some questions, if can help me I appreciate it.

  1. I have the solution index.ndx (water+cation+anion). Do I need to make a new index (water+cation)?

Are correct the following commands?
2) The command to set Na as reference would be:
gmx trjorder -f a.xtc -s a.tpr -n index.ndx -o b.xtc -na -da -com

  1. To calculate the SDF would be:
    gmx spatial -s topol.tpr -f b.xtc -n index.ndx -div -bin 0.08 -nab 50
4

Hi,

if one wants to order the water molecules (each water molecule is 3 atoms) around an ion, one needs an index file with a group with the ion (e.i Na ion) and a separate group with water molecules.
Then the command will be
gmx trjorder -f traj.xtc -s topol.tpr -n index.ndx -o order.xtc -na 3 -da 1

If one want to order according to the center of mass of the water molecules
gmx trjorder -f traj.xtc -s topol.tpr -n index.ndx -o order.xtc -na 3 -da 0

If the group to order is composed by molecules made by more than 3 atoms (e.i methane) than ‘-da 5’

'-com ’ uses the distance to the center of mass of the reference group

Regards
Alessandra