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.
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?
Thanks a lot!
Mu Xia,
Zhejiang University, China
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Received on Mon Apr 08 2013 - 19:30:02 PDT
