On Wed, Mar 25, 2015 at 7:41 PM, Glenn Carrington [bs10g3c] <
bs10g3c.leeds.ac.uk> wrote:
> Dear Amber users,
> I'm planning to run a large implicit solvent simulation of myosin using
> AMBER 12. I had a few questions that I was hoping someone could help me
> with.
> 1 - The molecule is quite big and I plan to use GPU's. The tutorials i
> looked at use a Langevin thermostat, but the GPU page states that this is
> very inefficient and I should use the Berendsen or Anderson thermostats. As
> the AMBER manual rules out the Berendsen due to issues with implicit
> solvent model, I guess I'm stuck with the Anderson (ntt=2). Could anyone
> with experience let me know the best setting for vrand (other than the
> default of 1000?) From what I've read this is the only variable associated
> with the Anderson thermostat?
>
I use Langevin dynamics all the time and I don't feel like it really has
that much of an effect on performance. Perhaps you should run a quick
timing comparison with Langevin dynamics and the Andersen thermostat to get
a better idea of the performance penalty you'll be facing?
> 2 - What settings do people use to equilibrate an implicit solvent
> simulation? Is the only consideration increasing the temperature from 0K to
> the
>
> target temp?
>
I usually use nmropt=1 and vary the target temperature linearly from the
starting temperature to the ending temperature over the course of tens- to
hundreds of picoseconds.
>
> 3 - Parts of the structure I'm using has been homology modelled. Are there
> any established protocols that anyone is aware of that I could use to test
> the stability of my structure?
>
RMSD isn't a bad place to start. If the RMSD is incredibly large for that
region, it's clearly not stable. Fluctuations can also help see if the
homology modelled loops are moving a lot.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 25 2015 - 19:30:02 PDT
