Dear Gromacs users,
I am currently working on a coarse-grained model where I want to fix atoms
(Cb's) on a certain distance from Ca-Ca bonds, so that they can rotate
freely. This freedom will be restricted by a dihedral that determines the
relative orientation between the Cb's.
I am using distance constraints or (non-chemical) bonds between a Cb and
the adjacent Ca's, so that a fixed triangle is formed. I assumed that with
this method the distance from Cb to the Ca-Ca bond should be correct and
that my problem was solved. However, sometimes my simulations crash, and it
appears that both constraint algorithms (LINCS and SHAKE) are not able to
deal with angle constraints / 3 atoms bonded in a triangle.
I came up with two (maybe very strange) idea to solve this problem:
1: There is a third algorithm to solve constraints, called SETTLE, but it
is stated almost everywhere that it is useful for water molecules. Do you
know if it is possible to use SETTLE in other molecules than water, for
example in my system? The Cb would be the "O", and the Ca's the "H's".
2: Is it possible to disable the constraint solver, so that neither Lincs
and Shake are used? I am asking this because someone mentioned that the
solvers are meant to reduce the very fast vibrations of light atoms, so
that a larger mass on my Cb's will also solve the problem.
For the method I want to use I really need the Cb's at fixed distances from
the Ca's and the Ca-Ca bond, but I cannot think of any way without
triangular constraints that fulfils these requirements.
Does any of you know the answers to the two possible solutions, or a way to
fix the distance between Cb and the Ca-Ca bond, while maintaining the free
Thank you in advance for any help!
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