How to use topology from CHARMM - GUI versus topology generated by pdb2gmx

User discussions
1

GROMACS version: 2020.01
GROMACS modification: Yes/No
Dear Gromacs users,
I am using the inflategro.pl to insert an ubiquinone molecule inside a popc lipid bilayer with 100 lipids generated using CHARMM-GUI. When I run the program initially:

perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat and then minimize the energy:

gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr
gmx mdrun -deffnm system_inflated_em

I visualized the system and the ubiquinone have been centered in the bilayer but the lipids are inverted: the polar head is pointing inside in the z direction instead pointing outside as it should be.

How could I fix this?

Kind regards,
Lazaro

2

Dear Lazaro,
This should not happen while using inflategro.pl code. You must see the starting coordinate you are using for inserting the molecule. The problem should be from there. You must take care of the box lengths. Maybe due to the PBC effect, you are getting such visualization.