Just to follow up on Crystal’s comments, 3D-RISM in the current release will not give the output you need for a direct comparison with GIST. This is in the works though. When it is available there will still be differences in the output due to the nature of the two theories. GIST is molecule based and distributions are for water molecules but RISM is a site-site theory, so contributions from hydrogen and oxygen are separated. This is something we are actively working on hope to have more to say soon.
Tyler
> On Aug 12, 2015, at 11:01 AM, Nguyen, Crystal <cnnguyen.ucsd.edu> wrote:
>
> 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 - 15:00:03 PDT
