[gmx-users] Gradual deformation of position-restrained structure
nedomacho at gmail.com
Tue Dec 20 00:25:54 CET 2016
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. Does this mean the -r makes
grompp pick up the list of restrained atoms from the topology and then load
their positions from the original.gro?
On Mon, Dec 19, 2016 at 4:17 PM, Mark Abraham <mark.j.abraham at gmail.com>
> gmx grompp -r original.gro
> permits you to keep your reference positions constant over all simulations.
> 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
> > 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
> > 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
> > 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
> > 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
> > 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
> > given that the atoms at the ends are restrained and not frozen and the
> > 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.
> > them? I know GMX something to freeze atoms, but never tried (and I think
> > is unphysical for our purposes)... Any other suggestions?
> > Thank you,
> > Alex
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