[gmx-users] RE : gmx-users Digest, Vol 113, Issue 106
ABEL Stephane 175950
Stephane.ABEL at cea.fr
Mon Sep 23 21:21:38 CEST 2013
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.
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 , 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 ).
>  www.ncbi.nlm.nih.gov/pmc/articles/PMC3133452/
>  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 A. Lemkul, Ph.D.
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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