Recently, I have carried out molecular dynamics simulation of quartz mineral surface. When I use NPT ensemble to simulate, I want to keep the mineral surface in place. When I followed the manual, I encountered the following problems. "Atom index (15) in position_restraints out of bounds (1-14).This probably means that you have inserted topology section "position_restraints"
in a part belonging to a different molecule than you intended to." How can I solve this problem？
I did not see the model, try the example in the exemple.docx
DR Rixin! The position restraint algorithm is used to restrain particles/atoms at a fixed reference position. Thus, an atom can move, but there is a large energy penalty for doing so.
http://www.gromacs.org/Documentation_of_outdated_version/How-tos/Position_Restraints#:~:text=The%20position%20restraint%20algorithm%20is,energy%20penalty%20for%20doing%20so.
Regards--
Dear Zhao Rixin,
This problem arises when the position restraint file/entry is misplaced in the topology file.
Please see the following page for a detailed discussion:
http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds
Best,
Felippe
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