AMBER Archive (2003)

Subject: Re: AMBER: Correction [Separation of a Water molecules]

From: nabe (watanabe-katsuhiro_at_hitachi-ul.co.jp)
Date: Wed Nov 12 2003 - 02:53:49 CST

not
> - anisotropic diagonal position scaling for pressure regulation
but
 - isotropic position scaling for pressure regulation

nabe wrote:
>
> Dear ALL.
>
> Thanks for reading question and replies!
>
> Carlos Simmerling wrote:
> >
> > this seems strange. you didn't give a lot of information.
> > what is the pressure at the start? at the end? are
> > you sure it is NTP? some information from the input
> > and output would help.
> >
>
> "Thomas E. Cheatham, III" wrote:
> > Likely you are running a constant volume simulation and the density is not
> > correct leading to a "vacuum bubble" forming. You need to equilibrate
> > with constant pressure first to make sure the density is stable/correct
> > first.
> >
> > If you were running constant pressure and see this problem, this is a more
> > serious issue...
>
> It declares first. This simulation was executed under
> constant pressure.
>
> <<the density profile>>
> 1. http://www004.upp.so-net.ne.jp/nabekatsu/MD0.jpg
> 0.823g/cc
>
> 2. http://www004.upp.so-net.ne.jp/nabekatsu/MD1.jpg
> 0.864g/cc
>
> 3. Intermediate state between 1 and 2 was shown in density
> 0.868g/cc (t=10ps).
>
> It becomes such graph.
>
> #Please view with a fixed font set ....
> # density
> # ^
> # | _
> # | / \
> # | / \
> # |/
> # +-------> state
> # 1 3 2
> #Please view with a fixed font set....
>
> It is that separation of water molecules arises
> between state of 3 and 2.
>
> <<input parameters>>
> I want you to understand a difficult point to provide
> a raw input parameter file to this place. Some input
> parameters is shown below on the assumption that the above.
> #################
> - using sander of amber5.
> - cell size ~ 80x80x80A^3
> - WATBOX216 for initial water molecules
> - constant pressure with boundary condition.
> - reference temperature is 300K
> - reference pressure is 1 bar (~ 1 atm)
> - Berendsen algorithm for Temperature regulation
> - anisotropic diagonal position scaling for pressure regulation
> #################
>
> Is a countermeasure in this phenomenon?
>
> Thanks.
>
> K. Watanabe (with automatic translation:)
>
> "Thomas E. Cheatham, III" wrote:
> >
> > > We have encountered the very serious problem. It is
> > > that the water molecules in the middle of MD
> > > separates. The links and explanations of pictures
> > > wrote below.
> > >
> > > Is a countermeasure in this phenomenon?
> >
> > Likely you are running a constant volume simulation and the density is not
> > correct leading to a "vacuum bubble" forming. You need to equilibrate
> > with constant pressure first to make sure the density is stable/correct
> > first.
> >
> > If you were running constant pressure and see this problem, this is a more
> > serious issue...
> >
> > \ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
> > | Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
> > | Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
> > | University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
> > |
> > | tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
> > \ BPRP295A / INSCC 418 http://www.chpc.utah.edu/~cheatham
> >
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