[gmx-users] Position restrain

[Maarten Wolf]

It is all about order. 

You have to include the position restraint .itp directly after the
molecule .itp (or inside the molecule.itp). 
If you place it behind the solvent .itp it will assume the position
restraints refers to the solvent.

The atom numbers in the position restraint should match the atom
numbers in the relevant molecule.itp

--- Alessandro Mattozzi <Alessandro at polymer.kth.se> wrote:

> mh, actually the status is like this: my system is made of two kind
> of molecules: one (solvent) with 12 atoms and the other with  more
> (thousands); i tried to run only with the "big" molecule and it works
> perfectly, it means the atoms restrained are those according to the
> index number; 
> when i introduce the molecule of solvent, it looks like I can lock
> only the solvent; how can I specify in the grompp the the position
> restrain refers to on .itp (the molecule) and not the solvent .itp? I
> thought that using atom index from the gro file would have worked....
> Thanks a lot! 
> Regards 
> 
> Alessandro Mattozzi
> M.Phil., Ph.D. student
> Dept. of Fibre and Polymer Technology
> Royal Institute of Technology
> Stockholm, Sweden
> 
> 
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org on behalf of Uwe Richter
> Sent: Thu 6/1/2006 11:33 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Position restrain
>  
> Hi,
> 
> 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, 
> however,
> 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,
> Uwe
> 
> 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. 
> >Thanx
> >
> >  
> >
> >>Regards
> >>
> >>Alessandro Mattozzi
> >>M.Phil., Ph.D. student
> >>Dept. of Fibre and Polymer Technology
> >>Royal Institute of Technology
> >>Stockholm, Sweden
> >>
> >
> >
> >  
> >
>
>------------------------------------------------------------------------
> >
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