[gmx-users] Generation of the Distance Restraints

[Mark Abraham]

On 22/03/2012 6:12 PM, James Starlight wrote:
> This days I tested some distance restrains applied on my protein. I 
> had some literature data  from wich I've used such restrains as well 
> as similar wirk where authors applied this data on the same protein to 
> view some biological-relevant event :)
>
> I've applied my restrains gradually to rise force from 0.1 to 30 kj nm 
> mol in mdp file.
>
> During such task I've noticed some disagreements between distances 
> wich I obtained after simulation as well as experimetnal data
>
> E.g in the topology file I've defined 2 restrains
>
>   1258 2203 1    15     1     0.450 0.650 1.600 1.0
>
>   1255 2742 1    16     1     1.900 2.150 3.150 1.0
>
> In this case this means that I defined first restrains betwenn 
> 0.45<r1< 0.65 where the value 1.600 is another threshold after wich 
> forses rise more gradually ( linnear). So I thought that the forces 
> must restrain the distance in the range between r0 and r1 most 
> strongly. The second restrain was chosen in the similar manner.

The position restraint forces are zero between r0 and r1, not 
restraining... "most strongly" there.

>
> But when I've checked output gro file I've found that real distances 
> between first two atoms were 0.800 nm (> 0.650) and betwen the second 
> pair of atoms 1.5 ( less than lowest R0 threshold 1.9 ).
>
> Why such disagreements have been occured ? Should I define restrains 
> range more accurately ? (e.g if I want to restrain atoms in the 
> distance equal to 0.5 nm so such harmonic restrains should be 0.45 
> 0.55 for r0 and r1 respectyally. )

If there's a car at the bottom of one valley in the Alps, and you think 
it should be two valleys over, and you pull it with a trained cat... 
it's not going to move much. How big an animal you need depends on the 
geography. There need not even be a reasonable route for you to take, if 
the target valley is effectively on Mars.

Mark