[gmx-users] Minimization question/problem

[Mark Abraham]

tprakci at ttnet.net.tr wrote:
> 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.

Indeed so... however one source of this problem is that where you think 
a bond should be isn't where the topology file specifies one is. Some 
visualization software will use its own heuristics to decide whether to 
show a "bond" between pairs of atoms, and there's no reason for them to 
correspond with your topology.

Mark