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 ================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
