[gmx-users] Constraining starting configuration in Coarse-Grain Simulation

[Maghesree Chakraborty]

Thank you for your response. I did not have tabulated potentials for bonded
interactions. I had tabulated potentials only for non-bonded
interactions. I had set constraints to be all-angles in my mdp file. I will
try using "constraint" interaction explicitly in my topology instead of
converting bonds and angles into constraints via mdp directive.

On Mon, Aug 7, 2017 at 1:58 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Tabulated bonded interactions are the opposite of constraints. You can
> explicitly use a "constraint" interaction type in your topology, which
> sounds like a good start. See chapter five of the reference manual.
>
> Mark
>
> On Mon, 7 Aug 2017 01:24 Maghesree Chakraborty <maghesree.c at gmail.com>
> wrote:
>
> > Hello,
> >
> > I am trying to run a CG simulation with only non-bonded interactions. I
> > have obtained the tabulated potentials for those interactions by
> > force-matching using VOTCA. I want all my bonds and angles to be
> > constrained as they are in the initial cg_conf.gro file. Since I do not
> > have tabulated potentials for bonded interactions, gromacs gives error
> if I
> > do not provide the bond and angle parameters (b0,kb and θ0 , kθ) in the
> > topology file. Then I tried setting the bond parameter (b0) to be the
> mean
> > of bond-length distribution in cg_conf.gro and the angle parameter (θ0)
> to
> > be the mean of the angle distribution in cg_conf.gro, I constrain the
> bonds
> > and angles with LINCS in my grompp file. During simulation, I get a lot
> of
> > LINCS warning and simulation is aborted. I am wondering if there is a way
> > of constraining the initial configurations of the molecules as they are
> in
> > cg_conf.gro file  in the absence of tabulated bonded potentials and not
> > forcing the molecules to have the bond-lengths and angles as specified
> by
> > the topology parameters.
> >
> > Thank you.
> >
> > Regards,
> > M. Chakraborty
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