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<P><FONT SIZE=2>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;<BR>
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....<BR>
Thanks a lot!<BR>
Regards<BR>
<BR>
Alessandro Mattozzi<BR>
M.Phil., Ph.D. student<BR>
Dept. of Fibre and Polymer Technology<BR>
Royal Institute of Technology<BR>
Stockholm, Sweden<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmx-users-bounces@gromacs.org on behalf of Uwe Richter<BR>
Sent: Thu 6/1/2006 11:33 AM<BR>
To: Discussion list for GROMACS users<BR>
Subject: Re: [gmx-users] Position restrain<BR>
<BR>
Hi,<BR>
<BR>
concept of 'molecules' as it is applied within Gromacs has been discussed<BR>
several times already, also with regards to distance restraints, which can<BR>
not be defined between different 'molecules'. Of course you can define<BR>
distance restraints between 'real' molecules by having the molecules<BR>
within the same topology block (atoms,bonds etc.), just without any<BR>
bonding parameters defined between them. Position restraints also have<BR>
to be defined for each topology block ('molecule') and are read in this<BR>
way by grompp. The index file .ndx referres to the atom numbering in the<BR>
structure file (.pdb .gro ...). The id's of the position restraints,<BR>
however,<BR>
refer to atom numbering within the 'molecule', starting from 1 for each, and<BR>
thus ,must be defined/included right after the corresponding 'molecule'<BR>
in the<BR>
.top file.<BR>
This is a little confusing and my chaotic description might not help a lot,<BR>
but it seems you have more than one 'molecule' in your system and the<BR>
one you want the position restraints for only has 12 atoms, even though it<BR>
might have the atom id 101 in your coordinate file.<BR>
<BR>
Best regards,<BR>
Uwe<BR>
<BR>
Alessandro Mattozzi wrote:<BR>
<BR>
>>While running a MD of PE with position restrain, i get this error message<BR>
>><BR>
>>Fatal error: [ file "posre.itp", line 6 ]:<BR>
>> Atom index (101) in position_restraints out of bounds (1-12)<BR>
>><BR>
>>My atom index goes up to 6000, why do I have to be in the 1-12 range?<BR>
>> <BR>
>><BR>
><BR>
><<your molecule only has 12 atoms and by the way, the error message is<BR>
><<from grompp.<BR>
><BR>
>actually my molecule has 12 thousand atoms, half of it dummies and half AUA. The .gro and .ndx contains atoms numbered up to 12000<BR>
>The error ideed comes from grompp.<BR>
>Thanx<BR>
><BR>
> <BR>
><BR>
>>Regards<BR>
>><BR>
>>Alessandro Mattozzi<BR>
>>M.Phil., Ph.D. student<BR>
>>Dept. of Fibre and Polymer Technology<BR>
>>Royal Institute of Technology<BR>
>>Stockholm, Sweden<BR>
>><BR>
><BR>
><BR>
> <BR>
><BR>
>------------------------------------------------------------------------<BR>
><BR>
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