[gmx-users] position restraints

[Justin A. Lemkul]

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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-- 
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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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