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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 Sat, Jun 13, 2015 at 1:48 PM, Ross Walker <ross.rosswalker.co.uk> wrote: > Hi Joe, > > For now you would need to modify the code for just the Z direction. We > have code internally for doing this but need to make the user interface > clean and generalized. Likely it will be released with the next version of > AMBER. > > All the best > Ross > > > On Jun 12, 2015, at 9:07 PM, Joseph Baker <bakerj.tcnj.edu> wrote: > > > > Hi Ross, > > > > Thanks. But those bugfixes just mean that now groups of atoms can be used > > in place of single atoms for the various iat(n) values, right? Does that > > update also allow for the nmropt distance restraint between the COMs of > > those two selections to be just in the z direction like you mentioned > > (e.g., a molecule above a membrane, for which you'd want to have umbrella > > windows along the membrane normal constraining the molecule to various Z > > values)? I thought that the distance restraint in the &rst namelist, > > whether it be between atoms or COMs of many atoms, does not restrain > along > > some direction. > > > > Kind regards, > > 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 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/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 Sat Jun 13 2015 - 17:30:02 PDT