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
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