How to insert molecules without overlap?

User discussions
1

GROMACS version: 2020.3
GROMACS modification: No

Hi there,

I want to insert a ball of 4 polystyrene chains with its center of mass at a specific coordinate in the solvated bilayer system that I’ve set up. I just need the ball to be below the membrane without overlaps. How can I do this?

I tried by straight-up concatenating the files and deleting the redundant box vectors, but ultimately there were so many issues. VMD couldn’t read it, energy minimization returned multiple LINCS errors, and there was atom overlap.

If anyone could help, I’d appreciate it tremendously!

Thanks!

2

Hi,

Maybe gmx insert-molecules could help

Kind regards
Alessandra

3

You should check out packmol software. It’s a good tool for preparing initial configurations.

1 Like
4

Hi Alessandra,

Is there a way to use gmx insert-molecules to place a molecule at a specific location. I can’t seem to find an option for that.

Thanks

5

Thanks for the suggestion! I just used it today and it works brilliantly!

1 Like
6

Hi,
Yes, you can insert the molecule at a specific location. See below an extract from the manual
"the molecules can be inserted at positions defined in the file positions.dat ( -ip ). That file should have 3 columns (x,y,z), that give the displacements compared to the input molecule position ( -ci ). Hence, if that file should contain the absolute positions, the molecule must be centered on (0,0,0) before using gmx insert-molecules (e.g. from gmx editconf -center ). Comments in that file starting with # are ignored. Option -dr defines the maximally allowed displacements during insertial trials. -try and -rot work as in the default mode "

Alessandra

7

Thanks!