[gmx-developers] Contributing new water models

Shirts, Michael R. (mrs5pt) mrs5pt at eservices.virginia.edu
Thu May 29 04:16:24 CEST 2014

I'm happy to manage putting this in for 5.1 if people want to add it.

Just wondering, what does the temperature dependent data look like compared to TIP4P-Ew or TIP4P/2005?  Those are better water models than the original TIP3P or TIP4P, but I only saw the single point data for those water models, vs. the temperature dependent properties in Fig. 3.

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

From: Lee-Ping Wang <leeping at stanford.edu<mailto:leeping at stanford.edu>>
Reply-To: "gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>" <gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>>
Date: Wednesday, May 28, 2014 at 1:11 PM
To: "gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>" <gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>>
Subject: [gmx-developers] Contributing new water models

Dear developers,

I'd like to contribute the following water models that were published in our recent article, "Building force fields - a systematic, automatic and reproducible approach."  The models, called TIP3P-FB and TIP4P-FB, are reparameterized versions of the TIP3P and TIP4P models; they have identical functional forms and computational cost, just different parameters.  They are highly accurate for reproducing the thermodynamic, kinetic and structural properties of liquid water across a wide temperature and pressure range.  The .itp files are attached in their final form.

I've run several microseconds of protein simulations using TIP3P-FB and TIP4P-FB, and they are highly compatible with the AMBER protein force fields (more specifically, amber99sb, amber99sb-ildn and amber99sb-nmr).  In fact, replacing TIP3P with TIP3P-FB tends to improve the stability of the "fast folding" proteins in D.E. Shaw's paper, and it also improves the prediction of NMR J-couplings and chemical shifts.  This is currently unpublished work but I'm working on a manuscript.

Please let me know if there's interest.  I think it could make sense to bundle this with the main Gromacs distribution, because the water models come with atom types that need to go into "ffnonbonded.itp" for the various implemented force fields.


- Lee-Ping Wang

Link to the paper: https://www.dropbox.com/s/phwlr3jsnhe46bw/Wang_Pande.RigidWater.JPCL.2014.pdf

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