FW: [gmx-users] position restraints

[abdullah ahmed]

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. 

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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