Hi Romelia,
In explicit solvent the helices of the dimeric helical bundle do not move
that much. In solution the helices at on one end of the bundle are
disordered but I 'm not seeing anything happening to them in my simulation.
I started from full helical structure, did 30 ns cMD and 4 ns aMD with the
following parameters:
Ed=Ed_average+4*ResNum
aD=4*ResNum*0.2
Ep=Ep_average+0.16*AtomNum
aP=0.16*AtomNum
In the manual is says that for a higher acceleration it is common to add to
Ed multiples of aD. What about the Ep and aP? Should these remain
unchanged? Could you please suggest possible changes to increase the boost?
thanks,
Thomas
On 19 November 2012 23:47, Romelia Salomon <romelia.caltech.edu> wrote:
> Hi Thomas!
>
> I only count real atoms, it is like a "per degree of freedom" thing.
>
> When I do implicit solvent I only use the boost on the dihedrals, that
> would be iamd=2
>
> Hope everything works fine :)
>
> > Hi Romelia,
> >
> > Thank you for your suggestions. I believe they will save other people as
> > well from "disoriented" experimentation with the aMD parameters.
> >
> > Each monomer has 80 residues and I 'm using the Amber99SB-NMR1-ILDN ff.
> > One
> > important detail I omitted is that my test simulations were done in
> > implicit solvent because I get 7x fold speed up compared with the
> original
> > system, which has TIP4P-Ew waters and ions and counts 134000 atoms in
> > total. Today I ran a couple of ns in explicit solvent and noticed that
> the
> > dimer is more stable, actually it doesn't move that much with the
> > suggested
> > parameter values. I will carry out more tests in explicit solvent and let
> > you know about the outcome.
> >
> > Just one last question, when I estimate Ep and aP values should I count
> > each TIP4P-Ew water as 4 atoms or as 3? So far I counted each water as 4
> > atoms.
> >
> > Thank you so much!
> >
> > Thomas
>
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Received on Thu Nov 22 2012 - 14:00:02 PST
