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From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Tue Apr 28 2015 - 10:06:28 CDT
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Miguel, you can truncate the density around your structure by using the
"volmap mask" command in VMD to create a binary mask, then multiply that
mask by your density using "volutil -mult".
On Tue, Apr 28, 2015 at 4:23 AM Miguel Caro <miguel.caro_at_aalto.fi> wrote:
> Dear all,
>
> I am working with charge density isosurfaces and have observed that for
> the cell size and grid spacing I'm dealing with these become memory
> intensive.
>
> I use big cells in my DFT calculations to prevent interactions with
> periodic replicas of my molecule. This means that the cell region where the
> wave functions are significantly different from zero is much smaller than
> the overall cell size. I was wondering if, in order to lower the amount of
> memory needed, I can somehow truncate the region in space where the
> volumetric data is represented to some region around my molecule, for
> instance by defining a spherical cutoff around some position in space.
>
> Many thanks,
> Miguel
>
> --
> *Dr. Miguel Caro*
> *Postdoctoral researcher*
> Department of Electrical Engineering and Automation,
> and COMP Centre of Excellence in Computational Nanoscience
> Aalto University, Finland
> Personal email: *mcaroba_at_gmail.com <mcaroba_at_gmail.com>*
> Work: *miguel.caro_at_aalto.fi <miguel.caro_at_aalto.fi>*
> Website: http://mcaroba.dyndns.org
>
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