Hi Thomas,
Indeed we are writing a paper together with Tyler Lucko who was the main Amber RISM developer on comparison between GIST and 3D-RISM. 3D-RISM does give significant different results than GIST especially for thermodynamics because GIST computes and output the energy and entropy on a voxel basis for a whole water molecule. Instead, 3D-RISM partitions these terms into atomic contribution, that is for oxygen and hydrogen atoms.
Tyler, please feel free to comment.
Crystal
________________________________________
From: Thomas Fox [thomas_fox.gmx.net]
Sent: Wednesday, August 12, 2015 8:36 AM
To: amber.ambermd.org
Subject: [AMBER] GIST vs. 3D-RISM
Hi,
as a follow-up to my previous post: are there any opinions about using GIST
vs. 3D-RISM (apart from computational cost), other than 3D-RISM gives a
clearly static picture (one uses just a single protein structure / snapshot)
whereas GIST is able to incorporate some aspects of flexibilty - although
usually the protein is more or less restrained to a single structure as
well...anybody done or published a comparison of the two methods?
Thanks,
Th.
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Received on Wed Aug 12 2015 - 11:30:03 PDT
