[gmx-users] Position restraint on DPPC lipid bilayer

Sithara Perera sithara.perera1993 at gmail.com
Thu Apr 6 11:45:15 CEST 2017


I'm really new to Gromacs and I' making a 512 DPPC bi-layer out of 128
bilayer available in http://www.cgmartini.nl. The force field used is

 But once the energy minimization is done, the bi layers crashes.

 So I made an position.itp file using the command

gmx genrestr -f dppc221.gro -n test.ndx -o lipid_posre.itp -fc 1000 1000

And included in the topology file. Topology file also include

include "martini_v2.0.itp"
#include "martini_v2.0_lipids.itp"  from martini.

 But then when the command

gmx grompp -f minim.mdp -c dppc221.gro -p dppc_bilayer.top -o em2.tpr

is given , following error occurs.

Fatal error:
[ file posre.itp, line 29 ]:
Atom index (25) in position_restraints out of bounds (1-24).
This probably means that you have inserted topology section
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.

How can I fix this?

Thank You,

More information about the gromacs.org_gmx-users mailing list