Hi Marc
Thanks for the help. I have a situation where i see some conformational
movement in a particular direction in protein (using classical MD), i want
to see for how much time does it continues the same path. I think what i
can do is run 2 simulations (one classical and one accelerated) to see if
there is some increase in the speed at which the protein changes
conformation. In this case i wont rely on mdinfo data but on actual motion
within the protein.
Meanwhile i will read the manual and references as you suggested.
Please correct me if my approach has error.
Please advice if there there is another way.
Regards
Abhilash
On Sun, Sep 11, 2016 at 2:03 PM, Marc van der Kamp <marcvanderkamp.gmail.com
> wrote:
> Dear abhilash,
>
> Accelerated MD is not magically giving you more simulation steps in the
> same time. The point is that the potential energy surface (and thus the
> free energy surface) is perturbed such that - with fewer simulation steps
> - you get conformational sampling that should be representative of much
> longer timescales.
> Please see the manual and the references therein.
> Your performance seems to be as expected.
>
> HTH,
> Marc
>
> On 11 Sep 2016 08:36, "Abhilash J" <md.scfbio.gmail.com> wrote:
>
> > Hi!
> >
> > I am trying to preform aMD on a system.
> > I was getting 8.06 ns/day using classical MD. When i tried using
> aMD,
> > the speed dropped to 6.38 ns/day.
> > My system has 238234 atoms (i.e. ~.2 million).
> > I am using TIP3P water in a box with periodic boundaries.
> > Protein being simulated is a dimer.
> > I am using a K20 GPU card for this simulation.
> > I am unable to understand why this speed drop happened when it
> should
> > accelerate and what can be done to fix this.
> > Please advice.
> >
> >
> > Regards
> >
> > Abhilash
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Received on Sun Sep 11 2016 - 02:00:03 PDT
