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

[Maghesree Chakraborty]

Hello,

Thanks for your reply.

Regards,
M. Chakraborty

On Mon, Aug 7, 2017 at 4:56 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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