On Mon, Apr 8, 2013 at 10:09 PM, Mu Xia <muxiachuixue.163.com> wrote:
> Hi all,
>
>
> I want to simulate a special "DNA" molecule which has a double-strands
> structure composed of non-natural base pairs. Experimental results show
> that when the number of base pairs reach 6, it could form stable
> double-strand, while not when the number is 4.
>
>
> In order to verify the experimental phenomenon, I have constructed two
> models and submitted them to MD simulations performed by AMBER11.
> The input is as following in the production phase:
>
>
> production
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=500000,dt=0.002,
> ntc=2,ntf=2,
> cut=10.0, ntb=2, ntp=1, taup=2.0,
> ntpr=500, ntwx=500,
> ntt=3, gamma_ln=2.0, ig=-1,
> temp0=300.0,
> /
>
>
> The ideal results would be that the 6-mer DNA remains stable in the MD
> simulation while the two strands of the 4-mer DNA separate at last. Here
> come my questions:
>
>
> 1. With the periodic boundary condition (ntb=2), is there any
> possibilities that the two strands of the special DNA could separate? I am
> afraid that the program will "pull them back" to the solvent box.
>
Sure, they can separate. With periodic boundary conditions keep in mind
that each strand can interact with all of the periodic images of the other
strand (specifically the ones in the adjacent periodic cells).
Therefore, you need to make sure that your simulation box is large enough
to allow the strands to separate as much as you want them to, keeping in
mind that the 'closest' strand may be its periodic image.
My guess is that you will have to do some kind of biased simulation to
capture any unfolding event, since I doubt you can simulate enough time to
catch it in regular MD.
> 2. In order to model the separation of the two strands, should the
> explicit solvent box be large enough? But this will increase the
> calculation time a lot definitely. Or could I use the implicit solvent
> (igb=1) here?
>
Implicit solvent models are not known to treat nucleic acid systems very
well. I would suggest sticking with explicit solvent if you can.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Apr 23 2013 - 19:30:03 PDT
