[gmx-users] Position restrain
Alessandro at polymer.kth.se
Fri Jun 2 12:09:04 CEST 2006
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!
M.Phil., Ph.D. student
Dept. of Fibre and Polymer Technology
Royal Institute of Technology
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
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'
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.
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
>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.
>>M.Phil., Ph.D. student
>>Dept. of Fibre and Polymer Technology
>>Royal Institute of Technology
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