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

Mark Abraham mark.j.abraham at gmail.com
Tue Dec 20 00:18:02 CET 2016


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 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
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list