[gmx-users] Generation of the Distance Restraints

James Starlight jmsstarlight at gmail.com
Thu Mar 22 08:12:04 CET 2012

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.

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. )

Thanks for help,

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