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.
On Wed, Apr 29, 2015 at 3:05 PM, Dr. Robert Molt Jr. <rwmolt07.gmail.com>
wrote:
> thank you!
>
> Dr. Robert Molt Jr.
> r.molt.chemical.physics.gmail.com
>
> On 04/29/2015 03:55 PM, David A Case wrote:
> > On Wed, Apr 29, 2015, Robert Molt wrote:
> >
> >> I apologize for this very elementary question, but I am having
> >> difficulty following parts of this conversation (and I would very much
> >> like to understand all of the wisdom imparted). It was written, below:
> >>
> >> "5ns windows is also fine, you might want to extend this to longer if
> >> that is easier for you to manage - I tend to try to shoot for 1 hour or
> >> so run time per simulation -"
> > I don't know why Ross does it this way, but it's just a matter of taste
> and
> > convenience. I generally target about 1 day per individual run: if a
> machine
> > crashes, I don't loose more than one day's calculation. But as long as
> your
> > script is automatically running job "n+1" as soon as job "n" is
> completed,
> > it's up to you how long each job lasts. There is no *scientific* reason
> to
> > prefer 1 hr vs 1 day vs 1 week.
> >
> > ....dac
> >
> >
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>
>
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--
Andrew Schaub
Graduate Program in Chemical & Structural Biology
Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/>
University of California, Irvine
Irvine, CA 92697-2280
949-824-8829 (lab)
949-877-9380 (cell)
aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
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Received on Wed Apr 29 2015 - 16:00:02 PDT
