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 :)<br>
<br>I've applied my restrains gradually to rise force from 0.1 to 30 kj nm mol in mdp file.<br><br>During such task I've noticed some disagreements between distances wich I obtained after simulation as well as experimetnal data<br>
<br>E.g in the topology file I've defined 2 restrains<br><br> 1258 2203 1 15 1 0.450 0.650 1.600 1.0<br><br> 1255 2742 1 16 1 1.900 2.150 3.150 1.0<br><br>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.<br>
<br>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 ).<br><br>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. )<br>
<br><br>Thanks for help,<br><br><br>James<br><br><br>