[gmx-users] RE : gmx-users Digest, Vol 113, Issue 106

[ABEL Stephane 175950]

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

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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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