Custom Search
-- Joseph Baker, PhD Assistant Professor Department of Chemistry C101 Science Complex The College of New Jersey Ewing, NJ 08628 Phone: (609) 771-3173 Web: http://bakerj.pages.tcnj.edu/ <https://sites.google.com/site/bakercompchemlab/> On Fri, Jun 12, 2015 at 5:26 AM, anu chandra <anu80125.gmail.com> wrote: > Thanks for the input, Jason and Ross. > > On Mon, Jun 8, 2015 at 5:17 PM, Ross Walker <ross.rosswalker.co.uk> wrote: > > > Hi Anu, > > > > > My queries are, > > > > > > 1. I wish to use lipid 14 and FF14SB force fields for membrane and > > protein > > > respectively. Will it be okay? Do I have to use any correction terms > > here? > > > I will be using POPC membrane. > > > > > > > Yes this is fine and no correction terms are needed. > > > > > 2. I have noticed in literature that , for microsecond long > simulations, > > > sometimes a 3 fs or 4 fs time steps were used. How safe to use such a > > large > > > simulation time step, though it reduce the use of computations > resource? > > > > > > > You can use 4fs time steps as long as you enable hydrogen mass > > repartitioning - see > > > > Hopkins C.W., Le Grand, S., Walker, R.C., Roitberg, A.E., "Long Time Step > > Molecular Dynamics through Hydrogen Mass Repartitioning", J. Chem. > Theory. > > Comput., 2015, 11 (4), 1864-1874, DOI: 10.1021/ct5010406 > > > > Although this has not been extensively tested with membranes. > > > > > 3. The membrane protein, I am working with, transport ions depend on > the > > > concentration gradient. In order to implement this in my simulation, I > am > > > planning to add ions ( for e.g KCl) in one of the leaflet to see the > > > movement of ions to the other leaflet through the pore. Am I making > sense > > > here, by restricting ion distribution to only one of the leaflet rather > > > than randomly placing in the entire simulation box (usually do for > > protein > > > simulation) at the starting of simulation? > > > > We are working on support for asymmetric boundary conditions that will > > effectively invert the symmetry in the Z direction allowing for ion > > gradients. At present though this is not released. Your only real option > > right now is to build a double bi-layer which will work fine but makes > you > > simulation larger and thus more expensive computationally. If you don't > do > > this then ions can just diffuse out the top of the box and thus appear in > > the bottom of the adjacent box and therefore mix without having to > traverse > > the membrane. > > > > > > > > 4. How can I build slab geometry boundary condition in Amber to > maintain > > > ion asymmetry? (http://www.ncbi.nlm.nih.gov/pubmed/12829468) > > > > > > > You would need to modify the code to support this. I would take a good > > look in the literature at the different methods people have tried before > > determining which is optimal. One thing that concerns me in the paper you > > reference here is the term: > > > > "It was shown recently that the Ewald method devised for systems with > > three-dimensional boundary conditions can also be applied to systems with > > slab geometry if the correct surface term is considered." > > > > Note the use of a 'surface term' - this is something completely > artificial > > and what everyone in the field developing lipid force fields has been > > working to move away from over the last several years. > > > > > > > > 5. If I would like to do membrane protein simulations with an applied > > > electric filed along Z-direction, how can I implement the electric > field > > in > > > Amber simulations? > > > > > > > Again you would need to add code to do this but it should not be too > > difficult and would be less work than changing the way the boundary > > conditions work. Although you'll need to figure out how to make this > behave > > correctly with PME. If you turn off PME then there is no warranty on the > > lipid parameters. ;-) > > > > > 6. Is it possible to do PMF calculation with classical MD trajectories > or > > > do I want to carried out umbrella sampling separately for PMF? > > > > > > > Yes you can do a PMF by using umbrella sampling. For example constraining > > the center of mass of the bilayer or protein to a molecule of your choice > > with the restraint just applying in the Z direction. Then just > reconstruct > > things with WHAM. > > > > > 7. Though I wish to use Amber for membrane protein simulation, some one > > > kindly provide some reference for membrane protein simulation where > Amber > > > used? ( sorry, I couldn't get one) > > > > > > > > > > https://scholar.google.com/scholar?cites=18167191384346104623&as_sdt=2005&sciodt=0,5&hl=en > > > > > > > https://scholar.google.com/scholar?cites=6723301433213089413&as_sdt=2005&sciodt=0,5&hl=en > > > > > > > https://scholar.google.com/scholar?cites=16304784273481526405&as_sdt=2005&sciodt=0,5&hl=en > > > > All the best > > Ross > > > > /\ > > \/ > > |\oss Walker > > > > --------------------------------------------------------- > > | Associate Research Professor | > > | San Diego Supercomputer Center | > > | Adjunct Associate Professor | > > | Dept. of Chemistry and Biochemistry | > > | University of California San Diego | > > | NVIDIA Fellow | > > | http://www.rosswalker.co.uk | http://www.wmd-lab.org | > > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk | > > --------------------------------------------------------- > > > > Note: Electronic Mail is not secure, has no guarantee of delivery, may > not > > be read every day, and should not be used for urgent or sensitive issues. > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Jun 12 2015 - 07:30:03 PDT