[gmx-users] position restraints

[Justin A. Lemkul]

abdullah ahmed wrote:
> Thank you for your reply,
> 
> I have been using [ position_restraints ], I do not know why it came out 
> that way in the mail.
> I agree with you, the problem probably comes from the position the code 
> lies in inside the .top file. I put it at the end of the file because I 
> thought that was the way it was supposed to be done. Perhaps this is 
> incorrect.
> 

That is incorrect.  The position restraints must belong to the [moleculetype] of 
the species to be restrained.  Once you #include a new molecule, you start a new 
[moleculetype] entry and the position restraints belong to it.  Putting it at 
the very end of a file probably has no effect whatsoever on any of the species 
in your system.

-Justin

> The final lines of the .top file are:
> 
> Include generic topology for ions
> #include "ions.itp"
> 
> [ system ]
> ; Name
> Protein
> 
> [ molecules ]
> ; Compound        #mols
> Protein_A           1
> 
> [ position_restraints ]
> 2 1 1000 0 1000 ;
> 3 1 1000 0 1000 ;
> 4 1 1000 0 1000 ;
> 5 1 1000 0 1000 ;
> 6 1 1000 0 1000 ;
> 7 1 1000 0 1000 ;
> 8 1 1000 0 1000 ;
> 9 1 1000 0 1000 ;
> 
>  
> 
>  > Date: Thu, 3 Jun 2010 09:00:36 -0400
>  > From: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] position restraints
>  >
>  >
>  >
>  > abdullah ahmed wrote:
>  > > Hello,
>  > >
>  > > I would like to restrain my molecule to a specific position in 
> space. I
>  > > would like for certain atoms to lie on the y-axis. To do this I used
>  > > the following code/lines in my .top file:
>  > >
>  > > [ position restraints ]
>  >
>  > This is an incorrect directive. It should be position_restraints.
>  >
>  > > 2 1 1000 0 1000 ;
>  > > 3 1 1000 0 1000 ;
>  > > 4 1 1000 0 1000 ;
>  > > 5 1 1000 0 1000 ;
>  > > 6 1 1000 0 1000 ;
>  > > 7 1 1000 0 1000 ;
>  > > 8 1 1000 0 1000 ;
>  > > 9 1 1000 0 1000 ;
>  > >
>  > > Unfortunately, after minimization my file contained the molecule in 
> the
>  > > same position as when the restraints were not applied.
>  > >
>  > > Does anyone know what I am doing wrong?
>  > >
>  >
>  > Perhaps the directive name is an issue, although I think grompp 
> should have
>  > raised a warning of some sort. Otherwise, is this block within the 
> appropriate
>  > [moleculetype] in the topology? Is it under control of an #ifdef 
> block that you
>  > haven't invoked in the .mdp file?
>  >
>  > -Justin
>  >
>  > > Thanks in advance,
>  > > Abdullah
>  > >
>  > > 
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>  >
>  > --
>  > ========================================
>  >
>  > Justin A. Lemkul
>  > Ph.D. Candidate
>  > ICTAS Doctoral Scholar
>  > MILES-IGERT Trainee
>  > Department of Biochemistry
>  > Virginia Tech
>  > Blacksburg, VA
>  > jalemkul[at]vt.edu | (540) 231-9080
>  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================