[gmx-users] Position restrain

Uwe Richter urichter at jerini.de
Thu Jun 1 11:33:28 CEST 2006


concept of 'molecules' as it is applied within Gromacs has been discussed
several times already, also with regards to distance restraints, which can
not be defined between different 'molecules'. Of course you can define
distance restraints between 'real' molecules by having the molecules
within the same topology block (atoms,bonds etc.), just without any
bonding parameters defined between them. Position restraints also have
to be defined for each topology block ('molecule') and are read in this
way by grompp. The index file .ndx referres to the atom numbering in the
structure file (.pdb .gro ...). The id's of the position restraints, 
refer to atom numbering within the 'molecule', starting from 1 for each, and
thus ,must be defined/included right after the corresponding 'molecule' 
in the
.top file.
This is a little confusing and my chaotic description might not help a lot,
but it seems you have more than one 'molecule' in your system and the
one you want the position restraints for only has 12 atoms, even though it
might have the atom id 101 in your coordinate file.

Best regards,

Alessandro Mattozzi wrote:

>>While running a MD of PE with position restrain, i get this error message
>>Fatal error: [ file "posre.itp", line 6 ]:
>>             Atom index (101) in position_restraints out of bounds (1-12)
>>My atom index goes up to 6000, why do I have to be in the 1-12 range?
><<your molecule only has 12 atoms and by the way, the error message is 
><<from grompp.
>actually my molecule has 12 thousand atoms, half of it dummies and half AUA. The .gro and .ndx contains atoms numbered up to 12000
>The error ideed comes from grompp. 
>>Alessandro Mattozzi
>>M.Phil., Ph.D. student
>>Dept. of Fibre and Polymer Technology
>>Royal Institute of Technology
>>Stockholm, Sweden
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