VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Mon Feb 26 2018 - 07:47:24 CST

Have you tried using domain restraints (an example is in the MDFF
tutorial)? This should help the domain fit together rather than the usual
piecemeal approach.

On Mon, Feb 26, 2018, 4:48 AM Rune Thomas Kidmose <rtk_at_mbg.au.dk> wrote:

> Hi all,
>
>
> I have been tinkering with MDFF for the past half year now, and I have
> accumulated a couple of questions, one of which is:
>
>
> Is it possible to somehow make MDFF handle large rotations of the initial
> model when fitting to the target density? It seems MDFF progresses quite
> linearly in its fitting, so is there a way to tell it or help it rotate
> e.g. a domain?
>
> I have come across a couple of cases where a domain clearly should be
> rotated significantly to fit the density, but MDFF just kept on pushing it
> into the density and then proceeded to fill the density by pulling in the
> domain. I am not thinking about iMDFF, where you manually interact with the
> model, which currently is the only way that worked for me.
>
>
> I acknowledge that rotation during MDFF it is not a trivial problem to
> solve but maybe I have missed some thing?
>
>
> Cheers
>
>
> Ruki
>
>
>