Also, some more recent work on simulating the stretching of DNA:
http://rsif.royalsocietypublishing.org/content/11/97/20140399
and references therein.
-Dan
On Mon, Dec 12, 2016 at 7:38 AM, Christina Bergonzo <cbergonzo.gmail.com> wrote:
> Hi,
>
> Dan Roe has done some DNA stretching/pulling simulations using AMBER:
> http://pubs.acs.org/doi/abs/10.1021/jp906749j
>
>
>
> On Mon, Dec 12, 2016 at 5:41 AM, Josh Berryman <
> the.real.josh.berryman.gmail.com> wrote:
>
>> Sarah Harris has done some DNA pulling simulations with amber eg here
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305225/
>>
>> In general I think you have to start and stop the simulations with new
>> restraint positions every 100ps or so (depending on restraint strength),
>> and try to make sure that you don't move the restraints too far too
>> suddenly.
>>
>> I'm trying to pull DNA myself at the moment, I've just sent a bug report to
>> devlist that restraints aren't working with the bleeding-edge versions of
>> pmemd.cuda.
>>
>> Josh Berryman
>>
>>
>>
>> On 12 December 2016 at 03:31, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>
>> > Not that I know of, and I looked into it for this by the way:
>> >
>> > http://phobrain.com/pr/home/mol.html
>> >
>> > Bill
>> >
>> > On 12/11/16 6:15 PM, The Cromicus Productions wrote:
>> > > I was thinking on fixing the first and last base pairs and using an
>> > > external force in order to make the helix become a stair. Is it
>> possible
>> > to
>> > > define external forces?
>> > >
>> > > On Sun, Dec 11, 2016 at 9:12 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>> > >
>> > >> E.g. high temperature is pretty easy to accomplish.
>> > >>
>> > >> Bill
>> > >>
>> > >>
>> > >> On 12/11/16 6:05 PM, David A Case wrote:
>> > >>> On Sun, Dec 11, 2016, The Cromicus Productions wrote:
>> > >>>> I want to simulate the untwisting of a DNA molecule. Is this
>> possible
>> > >> with
>> > >>>> AMBER?
>> > >>> You would have to decide what physical or artifical forces were
>> driving
>> > >> the
>> > >>> untwisting. The model those forces.
>> > >>>
>> > >>> ....dac
>> > >>>
>> > >>>
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>> > >>
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>> > >>
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>> >
>> >
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>
>
>
> --
> ---------------------------------------------------------------------------------------
> Christina Bergonzo
> Postdoctoral Researcher
> Department of Medicinal Chemistry, University of Utah
> http://home.chpc.utah.edu/~cheatham/
> ---------------------------------------------------------------------------------------
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Dec 12 2016 - 05:30:03 PST
