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

[Alex]

Come to think of it, you are correct about no problem with restraint, etc.
All that does is keep the initial references and what came out at the end
was compatible with them anyway.
Thanks a bunch.

Alex

On Mon, Dec 19, 2016 at 4:30 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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