AMBER Archive (2003)

Subject: Re: AMBER: Separation of a Water molecules

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Nov 13 2003 - 07:48:28 CST

I'm sorry we could not help.

in general, it is difficult to expect anyone to help
you if you can't even tell them what you are doing.
if you aren't an AMBER expert, you might not
actually be doing what you think you are doing.
without showing even your selection of input variables
you really are on your own.
good luck

----- Original Message -----
From: "nabe" <watanabe-katsuhiro_at_hitachi-ul.co.jp>
To: <amber_at_scripps.edu>
Sent: Wednesday, November 12, 2003 9:32 PM
Subject: Re: AMBER: Separation of a Water molecules

> 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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