[gmx-users] Position restraints problem

Jernej Zidar jernej.zidar at gmail.com
Wed Mar 28 09:52:51 CEST 2012

  After successfully importing a CHARMM-generated PDB file to GROMACS
I set out to do some short simulations. While all calculations
finished without a problem if everything but the water molecules were

  Removing the position restraints led to the system blowing up. Using
J. Lemkul's tutorial suggestion I generated an index file selecting
one lipid atom from sphingomyelin and one from cholesterol using
make_ndx and the selection: a P | a O3 (alternatively I tried also "6
| 7 | 17 | 18 | a P | a O3"). Any of the two selections selects only
atoms from the lipid part of the system.

  After creating the index file I used genrestr to position restrain
the movements of the selected atoms and obtain a position restrain ITP
file. I included this ITP file at the end of the lipid topology ITP
file as instructed on GROMACS' website.

 In the last step I edited the MDP file to use the position restraints
file for some lipid atoms but something went wrong as GROMPP
Fatal error:
[ file sys9-tmp-ions-mini-nofix-2-posre.itp, line 116 ]:
Atom index (12014) in position_restraints out of bounds (1-11954).
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.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

  Indeed, checking the lipid ITP file revealed there is no atom index
12014, yet there is an atom index 12014 (with the proper name) in the
GRO file (that I used to create both the index and the restraints
file) where all the atoms are listed. What have I done wrong?

Thanks advance,
Jernej Zidar

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