Re: [AMBER] Regarding GIST analysis

From: Steven Ramsey <>
Date: Tue, 22 Oct 2019 11:23:47 -0400

Hi Rabindranath,

Due to the way GIST calculates some quantities (entropy in particular) it
outputs quantities for all of the frames provided to the GIST command.
Therefore to obtain GIST quantities at differing simulation times you will
need to run separate GIST commands where each GIST command assesses a
different number of frames or a different segment of your simulation.

For example if you have 10,000 frames you want to assess and you want to
plot the translational entropy at every 1000 frames you would run 10
separate GIST commands, sum the quantities over the voxels of interest for
each GIST calculation, and plot the values for each of the 10 timesteps.

Hope this helps,


On Tue, Oct 22, 2019 at 3:12 AM MR. RABINDRANATH PAUL <>

> Dear all,
> In GIST analysis, one dx file contain data equal to number of
> voxels or number of grids.
> But, how can I get these thermodynamic properties along with simulation
> time (suppose I want to plot translational entropy vs simulation time)?
> Thanks in advance.
> With regards
> Rabindranath Paul,
> Senior Research Fellow,
> Department of Chemistry,
> Indian Institute of Technology Guwahati.
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Received on Tue Oct 22 2019 - 08:30:01 PDT
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