Finally, I have resolved my (little) problem: I used CHARMM-GUI to constructed 
the membrane, removed the TIP3 water molecules and then resolvate the bilayer 
with TIP4P/2005 water molecules. The simulation seems to work.

Stephane


 
On 9/23/13 10:23 AM, ABEL Stephane 175950 wrote:
> 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.
>

It sounds like you're on the right track, at least knowing that a considerable
amount of work has to be done to prove that the force field + water model
combination is sound.  Given that you're going to have to re-equilibrate the
water anyway, I don't see why you have to start with TIP3P and try to hack it
into becoming TIP4P; I would just strip the water and re-solvate.

-Justin

--
==================================================

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==================================================

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