[gmx-users] Gradual deformation of position-restrained structure

[Mark Abraham]

Hi,

On Tue, Dec 20, 2016 at 10:26 AM Alex <nedomacho at gmail.com> wrote:

> Well, that was very simple. : )
> Thanks Mark. I am just afraid that this may cause some funny behavior at
> the start of every new simulation, because the positions of the atoms next
> to the reference ones may be too far for the stability of the rather stiff
> C-C bond in graphene. Worth a try for sure.


I don't see why there'd be a problem if you just never turn the restraints
off. Note that you can also arrange the topology to restrain only in the
direction of selected axes.

Does this mean the -r makes
> grompp pick up the list of restrained atoms from the topology


Yes, as normal.


> and then load
> their positions from the original.gro?
>

Sure, like grompp -h says.

Mark


> Alex
>
> On Mon, Dec 19, 2016 at 4:17 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > gmx grompp -r original.gro
> >
> > permits you to keep your reference positions constant over all
> simulations.
> >
> > Mark
> >
> > On Tue, 20 Dec 2016 10:02 Alex <nedomacho at gmail.com> wrote:
> >
> > > Hi all,
> > >
> > > This is related to my previous question about trjcat (which Justin
> > answered
> > > perfectly) and now that it works, it has uncovered a problem. So, let
> me
> > > describe the system and what I am trying to do with it.
> > >
> > > I have a rectangular graphene membrane with approx. 4:1 aspect ratio,
> > > suspended at the ends. That is, two lines of atoms along the short
> > > direction at each end in the long direction are restrained to their
> > initial
> > > positions (k=50000 kj/mol/nm^2), which is part of the structure
> topology.
> > >
> > > The goal of the simulation is to periodically apply a constant
> > out-of-plane
> > > force to a single atom at the center of the ribbon, i.e. 10 ns on, 10
> ns
> > > off, etc. I couldn't find a way to do that in a single simulation, so I
> > > went with the cowboy version of it, i.e. I have an alternating sequence
> > of
> > > simulations from two mdp's, in one of which there is a constant force
> via
> > > pull code. Each subsequent simulation picks up the final gro of the
> > > previous and goes on. It works, thanks to Justin, and we are able to
> > track
> > > the deformation in terms of deflection at the center.
> > >
> > > Here is the problem: the small force during each "forced" step causes
> the
> > > ends shift ever so slightly toward each other, which makes the
> deflection
> > > increase in every subsequent force-on simulation. This is perfectly
> > normal,
> > > given that the atoms at the ends are restrained and not frozen and the
> > end
> > > structure of the (i-1)-th simulation is the beginning of the i-th, so
> the
> > > "pinned" positions keep shifting ever so slightly (but sufficiently to
> > > cause the observed artifact).
> > >
> > > What can we do? Is there a way to accomplish this force-on/force-off
> > > scenario in a single simulation?
> > > Is it possible to make the integrator omit a list of particles, i.e.
> > freeze
> > > them? I know GMX something to freeze atoms, but never tried (and I
> think
> > it
> > > is unphysical for our purposes)... Any other suggestions?
> > >
> > > Thank you,
> > >
> > > Alex
> > > --
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