On Mon, Apr 15, 2013, Hoshin Kim wrote:
>
> I am doing MD simulation on ssDNA in implicit solvent.
> As you can see the result through attached short movie, ssDNAs act like
> whirling helicopter's rotor.
> ntt=1, nsnb=20, offset=0.13, ntr=1,
Don't use ntt=1 for implicit solvent simulations (see the discussion on the
ntt variable in the Users' Manual). I've a suspicion that you
have energy drains (coming from using a shortish cutoff for electrostatics)
and energy is going into overall motion. See if going to ntt=3 changes
things. I'd also suggest a longer cutoff, even at the expense of longer
simulation times.
....dac
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Received on Tue Apr 16 2013 - 05:00:03 PDT
