Hi,

If there's no interactions with CB then what's the point?

Mark

On Tue, Mar 13, 2018, 09:28 Douwe Pollmann <douwepollm...@gmail.com> wrote:

> Hi Mark,
>
> Thanks for your reaction!
>
> 2018-03-12 18:08 GMT+01:00 Mark Abraham <mark.j.abra...@gmail.com>:
>
> > Hi,
> >
> > On Mon, Mar 12, 2018 at 4:19 PM Douwe Pollmann <douwepollm...@gmail.com>
> > wrote:
> >
> > > 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.
> > >
> >
> > 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
> solution..
>
>
> >
> > > 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
> > to
> > > fix the distance between Cb and the Ca-Ca bond, while maintaining the
> > free
> > > 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!
>
>
> >
> > Mark
> >
> > Thank you in advance for any help!
> > >
> > > Kind regards,
> > > Douwe Pollmann
> > > --
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