I have performed simulations on nucleic acids using both implicit and
explicit. In my case explicit solvent worked perfectly fine. But implicit
solvent model didn't give satisfactory results since the model was not
stable. So, I would recommend explicit solvent.
mani
On Mon, Jan 28, 2013 at 9:38 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Mon, Jan 28, 2013 at 9:04 AM, Debayan Chakraborty
> <debayan.ch.gmail.com>wrote:
>
> > Dear AMBER users,
> > From the AMBER archives I gather that
> > implicit solvent simulations using models such as GB with explicit ions
> are
> > not recommended, but I am trying to simulate a G quadruplex which
> requires
> > potassium ions to hold the stacks together (in fact I tried simulations
> > with GB and salt effects taken implicitly but they did not give the
> correct
> > stacking ). The potassium ions that were initially placed in the core of
> > the quadruplex were expelled during the simulations with GB. Has anyone
> > experienced the same problems, and give suggestions as to what could
> > possibly be done to circumvent this ?
> >
>
> I would suggest against using GB for nucleic acid simulations. igb=1 has
> shown stable dynamics for NAs in the past, I think, but I think the general
> consensus is that you need explicit solvent generally. I would argue this
> is _especially_ true if you have structural ions.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Manikanthan Bhavaraju
> Graduate Teaching Assistant
> Dept. of Chemistry
> Mississippi State University
> office no : 662-325-4633
> MS -39762
> USA. <http://lists.ambermd.org/mailman/listinfo/amber>
>
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Received on Mon Jan 28 2013 - 08:00:03 PST
