On Wed, Apr 29, 2015, Andrew Schaub wrote:
> I've been following this scheme for my longer production runs (
> http://archive.ambermd.org/201103/0431.html):
> 1) Heat system using NVT (ntb=1,ntp=0,ntt=3,gamma_ln=1.0) [20 ps]
> 2) Equilibrate the system using NPT (ntb=2,ntp=1,ntt=3,gamma_ln=1.0) [5 ns]
> 3) Production using NVT (ntb=1,ntp=0,ntt=1,tautp=10.0).
>
> So I'll start with NTT=3 for 5 ns, then switch to NTT=1 for the rest of the
> simulation.
This could get to be a *long* discussion, but since people consult the
archives a lot, and since the title is about "microsecond simulations", a few
notes:
1. Most biomolecular systems take more than 5 ns to converge. A small
protein molecule will not even have had time to randomize is overall
orientation (undergo rotational tumbling) on this time scale. Of course,
perceptions change as computers get faster, but your schedule treats only
0.5% of the total microsecond run as "equilibration". This seems too small to
me.
2. Using ntt=1 can save some time relative to ntt=3, but I'm not convinced
that is a good tradeoff. In principle, ntt=2 should be a good compromise,
speeding up the calculation, avoiding both energy drifts and subtle problems
that can arise with ntt=1. Problem is that I don't have very much *personal*
experience with ntt=2; others might want to chime in here. (I suspect that
Amber needs a better "shake-aware" velocity randomization procedure....)
3. If you use ntt=3, in most cases you should set ig=-1. If you set ig to
some other value, be sure you understand what you are doing, and why.
....dac
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Received on Thu Apr 30 2015 - 05:30:02 PDT
