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

Mark Abraham mark.j.abraham at gmail.com
Mon Aug 7 19:58:45 CEST 2017


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.


On Mon, 7 Aug 2017 01:24 Maghesree Chakraborty <maghesree.c at gmail.com>

> 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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