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. Stephane 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 -- ================================================== 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
