# Re: AMBER: Separation of a Water molecules

From: nabe <watanabe-katsuhiro.hitachi-ul.co.jp>
Date: Wed, 12 Nov 2003 17:43:59 +0900

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.utah.edu (801) 587-9652; FAX: (801) 585-9119
> \ BPRP295A / INSCC 418 http://www.chpc.utah.edu/~cheatham
>
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Received on Wed Nov 12 2003 - 08:53:01 PST
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