VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 22 2014 - 11:33:40 CDT

Hi,
  One of my colleagues wrote the rotation logic, so I don't know the
answer to your first question (1) off the top of my head. For (2), one
reason that you might not want to rotate the system is that some people
don't want the system rotated vs. some starting orientation if they are
planning on comparing the simulation trajectory vs. some other, e.g.
externally provided, structure or simulation box that's in a different
orientation. The point is that the user needs to know what they are
trying to do, and whether it is appropriate to allow the solute structure
to be rotated or not. The program should not be making arbitrary
decisions that more rightly belong to the scientist preparing the
simulation, particularly decisions that may have important side
effects. Another concern with reducing the water volume is that one
can end up going too far and creating problems with interations between
the periodic images, the user preparing the system has to know what
is likely to happen during the simulation, if the solute is spherical
and doesn't unravel in the simulation, then a rotation to reduce volume
might be perfectly safe. On the other hand, if it is an unfolding
simulation, or a structure that is asymmetric, allowing the solvate tool
to rotate the structure automatically might be a very poor idea.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 22, 2014 at 04:59:35PM +0200, Sebastian Stolzenberg wrote:
> Dear All,
>
> 1.)
> In the Solvate Plugin, I came across the
> ::Solvate::rotate_save_water
> procedure, which rotates a given system along the z and x axes to find
> the orientation with minimum surrounding cuboid volume V0.
> I was wondering why this rotation is not performed along all three
> cartesian axes to allow the algorithm to find even smaller values of V0.
>
> As an example, I am attaching a tcl script I wrote to execute this task
> for the "2D8R" PDB structure:
> As a result, I obtain a 15% reduced volume compared to the one obtained
> from ::Solvate::rotate_save_water.
> When I further solvate this system with a 20A water buffer layer (not
> shown), the total number of atoms is reduced by 29% compared to the
> solvated system produced by the solvate plugin.
>
> 2.)
> At http://www.ks.uiuc.edu/Research/vmd/plugins/solvate/
> I read:
> "Because the solvation box must be oriented along the cardinal axes,
> this can result in significant system size reductions, but should not be
> used if the initial orientation was chosen to facilitate analysis"
> I don't quite understand the last half sentence, what kind of situations
> does it specifically refer to?
>
> Thank you very much, Best,
> Sebastian
> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/