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, James
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