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

[Mark Abraham]

Hi,

Ok, I didn't understand you because I didn't have enough information yet.
IIRC your topology will still have to specify the constraint bond length,
you can't have grompp infer it from the starting coordinates. You should
also get a single molecule working correctly, because the symptoms of
broken topology and broken initial coordinates are often not
distinguishable. Prove the topology first when there cannot be an
inter-molecular clash.

Mark

On Mon, 7 Aug 2017 22:00 Maghesree Chakraborty <maghesree.c at gmail.com>
wrote:

> 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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