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In my simulation setup involving a silica nanoparticle (NMB), I encountered issues at nvt equilibrium due to the absence of a posre.itp file, resulting in the following errors during simulation setup:
ERROR 314 [file NMB.itp, line 21]: No default Position Rest. types
ERROR 315 [file posre.itp, line 6]: Atom index (2) in position_restraints out of bounds (1-1).
Facing this challenge, I sought to generate a posre.itp file for my silica particles. To do so, I employed the make_ndx and genrest commands, following commonly suggested procedures. However, despite my efforts, this approach did not yield the desired outcome, and the issues persisted.
Can anyone help me with this errors?
Hi, it seems that your original posre.itp was malformed or misplaced for whatever reason - the error suggests it was included in a single-atom [ moleculetype ] so that atom index 2 is out of bound. Remember that a position restraint section will belong to a given molecule based on separation by [ moleculetype ] headers, and the indices will be matched against ones defined in its molecule’s [ atoms ] section.
In principle, there’s nothing complicated in creating a (conditional) [ position_restraint] entry by hand and wrapping it in a conditional #ifdef POSRES and #endifcommands, just follow the format from any correctly formed topology.
That being said, there’s both a gromacs tool and a gromologist command to add position restraints to existing topologies, so choose which way works for you best.
Hello again i used gromologist and tried to add posres to my topol with this command : " t.add_posres(keyword = ‘POSRES’, value = 1000) "
and encountered this : " [ position_restraints ] already present in molecule CR2, skipping" i dont know why this happens and how to overpass it , is this because i tried to restrain atoms with genrester command before or because of sth else?
@milosz.wieczor
Hello again i used gromologist and tried to add posres to my topol with this command : " t.add_posres(keyword = ‘POSRES’, value = 1000) "
and encountered this : " [ position_restraints ] already present in molecule CR2, skipping" i dont know why this happens and how to overpass it , is this because i tried to restrain atoms with genrester command before or because of sth else?
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If it says it’s already present, then remove it from the file and add it from scratch. This check is to prevent users from unknowingly adding new restraints on top of already existing ones.
my system doesnt have a restraint file and I havent included any restraints in my topology file so how does this happens?
@milosz.wieczor
When you run add_posres on the whole topology, it will go through all defined molecules that have > 5 atoms, and try to add a position_restraints section to them. It might print this message when it encounters a chain that already has the section, but it should anyway add the restraints to other molecules - that might be what happened to you.
If that’s not the case, then create a standalone topology file (just read and save the .top with Gromologist) and search within the file for “position_restraints”, it might be hidden somewhere as a nested #include.