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 |
> ---------------------------------------------------------
>
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Received on Fri Jun 12 2015 - 02:30:04 PDT
