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.
>>>
>>>
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Received on Fri Jun 12 2015 - 20:00:02 PDT
