[gmx-users] angle_restraint_z

Karina karinapi at mail.tau.ac.il
Tue May 24 16:40:12 CEST 2016


I am trying to restrain the angle between two atoms (type a5) in a half
spherical body with respect to the z axis. I am trying to use
angle_restraint_z, but not sure how to do it correctly due to lack of
information in the manual or in forums.

I have created a .itp file with  angle_restraint_z and included it in the
topology file as follows:

#include "a5.itp"
#ifdef ANGRESZ
#include "angrez-a5.itp"

and in the .mdp file as follows:
define       =-DANGRESZ

The problem is I get the following error

Fatal error:
[ file angrez-a5.itp, line 5 ]:
Atom index (3384) in angle_restraints_z out of bounds (1-1).
This probably means that you have inserted topology section "angle_restraints_z"
in a part belonging to a different molecule than you intended to.
In that case move the "angle_restraints_z" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

The only way I can run it is if my indexes are 1 in my .itp file:

[ angle_restraints_z ]
;i j   funct   theta0   fc   mult
 1 1    1    90    100000  1

which is incorrect.

Can you please help me understand how to do it correctly?

Thank you.

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