[gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?
douwepollmann at gmail.com
Tue Mar 13 09:27:54 CET 2018
Thanks for your reaction!
2018-03-12 18:08 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
> On Mon, Mar 12, 2018 at 4:19 PM Douwe Pollmann <douwepollmann at gmail.com>
> > Dear Gromacs users,
> > I am currently working on a coarse-grained model where I want to fix
> > (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
> > 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
> > appears that both constraint algorithms (LINCS and SHAKE) are not able to
> > deal with angle constraints / 3 atoms bonded in a triangle.
> You should double check the documentation of the mdp options relevant to
> these algorithms so that you know you are using them correctly - triangles
> of constraints are more demanding than uncoupled ones.
I will play a bit more with the values for lincs-order and lincs-iter, or
the value for shake-tol.
> You should also make sure that your exclusions are appropriate. If the Cb
> atom is having a non-bonded interaction with the Ca atoms (or their
> neighbours) then you make life hard on the constraint implementation.
There is no interaction with the Cb's and the other atoms in the system, I
excluded them all in the energygrp-excl. So unfortunately that isn't the
> > 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".
> No, SETTLE is specific to water, ie. molecules with three heavy atoms.
> > 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.
> If you don't want constraints, don't ask for any :-) You also won't get
Yeah okay, true :)
> your fixed triangle. You can of course do that, with due regard to your
> timestep and validation of your module.
> 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
> > fix the distance between Cb and the Ca-Ca bond, while maintaining the
> > rotation?
> The ideal answer would be to use a virtual site in GROMACS, but there's no
> way of constructing the Cb atom off the line of the two Ca atoms. There are
> ways to construct the Cb atom on the line, or various ways from the
> positions of three or more other atoms, but nothing is clearly suitable for
> your case, unfortunately.
I also thought of virtual sites and I came to the same conclusion as you,
so I was already afraid for this answer..
Thanks for thinking along!
> Thank you in advance for any help!
> > Kind regards,
> > Douwe Pollmann
> > --
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