One odd thing (and maybe I'm wrong about this), but if you are doing ntt=3
(langevin dynamics) it relies on a parameter gamma_ln, which is apparently
set to 0 by default even when ntt=3, and in that case you are essentially
not doing langevin dynamics. I can't really imagine that the default would
be 0 as that must mean a number of people think they are running langevin
dynamics and are not, but that was my impression from the manual. So
anyway, I suggest you set gamma_ln to be something, I think the manual has
recommendations (2 for instance).
In terms of equilibration and production, it really depends on your
system. If your system is a just a box of water with ions and a protein or
something of the sort, I would recommend doing equilibration with NTP in
order to get the periodic box dimensions correct (correct density and
pressure), and then doing the production with NVT since you'll gain ~15%
speed from taking out the pressure control calculations and you've already
got the box dimensions right. But it really depends on your system.
On Sat, Feb 18, 2012 at 6:39 AM, Atila Petrosian
<atila.petrosian.gmail.com>wrote:
> Dear amber users
>
> If I want to do only 2 steps (equilibration and production run) after
> minimization, which one is the best?
>
> 1- eq (NVT) 2- prod (NPT)
>
> or
>
> 1- eq (NPT) 2- prod (NPT)
>
>
> Best regards.
>
>
> On Sat, Feb 18, 2012 at 2:32 PM, Atila Petrosian
> <atila.petrosian.gmail.com>wrote:
>
> > Dear amber users
> >
> > I want to know what parameters are needed in input file for NVT and
> > NPT simulation.
> >
> > In my opinion:
> >
> > NVT:
> >
> > ntb = 1, ntt = 2 or 3
> >
> > NPT:
> >
> > ntb = 2, ntt = 2 or 3, ntp = 1 or 2
> >
> > Are they true and enough?
> >
> >
> > Any help will highly appreciated.
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Feb 18 2012 - 06:30:02 PST
