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.
>>>>>
>>>>>
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Received on Sat Jun 13 2015 - 11:00:02 PDT
