[gmx-users] Minimization question/problem

[tprakci at ttnet.net.tr]

Thank you,
Sorry for the second post of the same question. 
As I understood, my molecule seems to have a distorted structure initially. This caused some bonds to distort further during minimization. Can I ask, Why LINCS could not prevent it? In the manual it writes:

-LINCS is an algorithm that resets bonds to their correct lengths after an unconstrained update [28]. The method is non-iterative, as it always uses two steps.-
-Even when it is impossible to to reset the constraints LINCS will generate a conformation which fulfills the constraints as well as possible.-

This correct length should be the length in the topology file I think.