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-- 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 10:46 PM, Ross Walker <ross.rosswalker.co.uk> wrote: > Hi Joe, > > See updates 10 and 11 to ABER 14. :-) > > http://ambermd.org/bugfixes14.html > > All the best > Ross > > > On Jun 12, 2015, at 7:25 AM, Joseph Baker <bakerj.tcnj.edu> wrote: > > > > Hi all, > > > > Ross, I noticed in this thread you just mentioned that > > > > """> 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.""" > > > > My understanding from the manual and some previous threads is that a > > restraint just applied along the Z direction is not possible in pmemd or > > pmemd.cuda, but just in sander (through the . Am I wrong? This would > > actually be very helpful for some simulations I want to run looking at > > molecules moving through membranes. > > > > Thanks, > > Joe > > > > > > -- > > 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/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 - 21:30:02 PDT