Dear all,
I am doing MD simulation on ssDNA in implicit solvent.
As for my part of research, I am trying to do MD using ssDNA where one end
of ssDNA is harmonically constrained in order to assume that DNA is grafted
on the surface.
As you can see the result through attached short movie, ssDNAs act like
whirling helicopter's rotor. Also, unlike implicit simulation using same
ssDNA without restraint, No folding, unfolding of strcuture occur during
simulation.
Since I have Amber 10 to 12, I did same simulations using different version
of Amber. But Results look same except for Amber 10 (Blue one in the
movie).
I used same input file mentioned below;
&cntrl
imin=0, ntx=5
irest=1, ntxo=1, cut=15.0, tempi=300.0,
ntpr=1000, ntwx=1000, ntwe=1000,
nstlim=20000000, tautp=2, temp0=300.0,
dt=0.001, nscm=100,
igb=1, ntb=0, saltcon=0.5, gbsa=1,
ntt=1, nsnb=20, offset=0.13, ntr=1
restraint_wt=5.0,
restraintmask='.1-2',
/
(I also tried to use below command to constrain atoms, but result showed
same problem.)
(&end
GROUP FOR CONSTRAINTS
5.0
ATOM 1 2
END
END
)
Since I don't want to use Amber 10 now, I will appreciate it a lot if
anyone tell me how to figure out this conformational problem.
Regards,
Hoshin Kim
P.S: In the attached movie;
Blue (Result from Amber 10 SANDER)
Red (Result from Amber 11 SANDER)
Green (Result from Amber 12 PMEMD, SANDER gave me same result)
P.S2: I reduced the size of movie due to limitation of amber archive. (less
than <1024kb) I wish you all have no visual problem to watch it
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Received on Mon Apr 15 2013 - 15:30:03 PDT
