Re: [AMBER] time scales for running MD

From: Carlos Simmerling <>
Date: Mon, 1 Sep 2014 11:50:23 -0400

not really. imagine that you instead carried out 600,000 simulations of 1ps
each (still 600ns total). none will go far from the initial structure and
you would not expect to see motions that occur in 600ns. the issue is
somewhat complex, and depends a lot on whether you are looking at something
that obeys first orders kinetics and so on. the folding.home people have
done a lot of work in this area, since they tend to have many relatively
short simulations. Also, even if it is first order kinetics, the rate
constant will determine a probability of seeing an event in a certain
timescale. our simulations do not normally have the number of independent
events needed for them to show statistical behavior that might match up to
an experiment on a particular timescale. so, as Dave Case mentioned, if the
"events" that you see occur on a similar timescale to the length of the
simulation, you an't say much specific about whether another simulation
would or would not see the same behavior, or if it is significant that
another simulation does not.

In your specific case, you should probably look into what others have seen
in their simulations of loops, since a fair number of studies have been
published in that area. I agree with DAC, 200 or even 600ns is not very
long. Much depends on the initial structure and what type of dynamics you
are trying to study.

On Mon, Sep 1, 2014 at 9:38 AM, Asmita Gupta <> wrote:

> But, then i have 3 different runs for the same system, each 200ns. Is it
> incorrect to say that the system has experienced conformational sampling
> for a total of 600ns, which might be long enough for loops?
> Asmita
> On Mon, Sep 1, 2014 at 5:54 PM, David A Case <>
> wrote:
> > On Mon, Sep 01, 2014, Asmita Gupta wrote:
> > >
> > > In 2 out of 3 trajectories, the structure is experiencing a loop
> residue
> > > backbone flipping (zeta, chi and delta), after which it remains stable.
> > > However, with parmbsc0, this residue flipping is not observed at all,
> > > neither with YIL chi correction.
> >
> > One useful analysis is to see how long it took for the flip to take place
> > in
> > the two trajectories where it did happen. If these are significant
> > fractions
> > of the 200 ns length, then it is plausibly just a matter of chance that
> you
> > did not see such behavior in the third run. You could extend the third
> run
> > longer to see what happens.
> >
> > >
> > > is 200ns enough for a good conformational sampling?
> >
> > This is not sufficient in general to sample RNA loop configurations.
> >
> > ....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> >
> >
> >
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Mon Sep 01 2014 - 09:00:02 PDT
Custom Search