[gmx-users] script to convert the TIP3P water model into TIP4(P)/2005

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Mon Sep 23 16:23:33 CEST 2013

Hello Justin,

Thank you for your response and your interest for my simulations ;) I am of course aware that the "primary" water model for the CHARMM is the TIP3(S)P model. 

Since, I am mainly interested to the water dynamic around DOPC molecules in the context of the different water/DOPC mesophases (not data available, I currently doing the tests ;)) and that it is known that the TIP4P/2005 water model (it is the model, I want to use) reproduces better the water dynamic and structure than the TIP3P water model, I would like to test if the TIP4P/2005 water can be used in simulation of membranes. I am not aware that somebody have already done the test. 

Finally, Justin, you are probably right here, the results will be probably not good as it is suggested by Pastor and MacKerell in their paper for TIP4P-EW water model [1], but I think that it is worth a test to confirm this in case of the TIP4P/2005. I am not the first one to ask this question in the context of simulations with the CHARMM force field (for protein, here [2]).

[1] www.ncbi.nlm.nih.gov/pmc/articles/PMC3133452/
[2]  Nutt, D. R.; Smith, J. C. Molecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied? J. Chem. Theory Comput. 2007, 3, 1550–1560.


On 9/23/13 5:02 AM, ABEL Stephane 175950 wrote:
> Hello,
> Because I want to compare the simulation results (essentially water dynamic) with previous simulations of reverse micelles, micelles carried out with the same water model.

The math for producing the virtual site in TIP4P is described in tip4p.itp, so
you can use that.  What's more curious is that if a paper claims to use TIP4P
but the provided files use TIP3P, then either there has been a mix-up in the
files or an error in the paper.  In either case, I find it odd to use TIP4P with
CHARMM, especially given the sensitivity of lipid parameters to the water model.
  Without knowing the paper you're talking about, I will not criticize the
choice as it may have been justified.  It's probably a good question to ask of
the corresponding author of the study you are trying to reproduce.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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