AMBER Archive (2003)

Subject: Re: AMBER: Separation of a Water molecules

From: nabe (watanabe-katsuhiro_at_hitachi-ul.co.jp)
Date: Wed Nov 12 2003 - 20:32:45 CST

Dear Carlos Simmerling.

 Thank you for a reply.

 Since our customer's permission is required,
it is very difficult to offer raw input file.
I am very sorry.

-About your proposal
 Although I performed calculation using various
value for a coupling constant, I failed.
I think that there is another problem against
coupling constant one. So I will continue
the investigation about this problem.

Since I think I won't get more information about
this problem, I want to finish this discussion
here. If there is an opinion about this problem,
please send it to my E-mail address.

If this cause and solution are found, I will write again.

Thanks.

K. Watanabe (with automatic translation:)

Carlos Simmerling wrote:
>
> why can't you insert your input file? it would
> be easier for us. the initial density is low, maybe you
> should use a smaller coupling constant for equilibration.
> I can't tell what you used since you didn't provide
> the input file.
>
> ----- Original Message -----
> From: "nabe" <watanabe-katsuhiro_at_hitachi-ul.co.jp>
> To: <amber_at_scripps.edu>
> Sent: Wednesday, November 12, 2003 3:43 AM
> Subject: Re: AMBER: Separation of a Water molecules
>
> > 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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