From: Axel Kohlmeyer (
Date: Tue Apr 28 2015 - 10:41:55 CDT

On Tue, Apr 28, 2015 at 11:06 AM, Ryan McGreevy
<> wrote:
> 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".

i don't think that that will reduce the file size and/or storage
requirements (on the contrary).
a long time ago i wrote a utility that can perform such grid cutting
operations on gaussian style cube files.
i am attaching the (C) source code. it can do some additional
processing and trimming as well.
of course, if your grids are in a different format, you will need to
change the parts related to reading the data.


> On Tue, Apr 28, 2015 at 4:23 AM Miguel Caro <> 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:
>> Work:
>> Website:

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.