[gmx-users] Help!

[Ankur]

Hi Gromacs Users,

I dissolved my protein in water and now want to calculate the diffusion
coefficient of water near and far away from the protein. I tried but was
unsuccessful. Can anybody tell me how should I approach this problem? I
would really appreciate that.

Sincerely
Ankur

----- Original Message -----
From: "David" <spoel at xray.bmc.uu.se>
To: <gmx-users at gromacs.org>
Sent: Friday, February 20, 2004 7:15 AM
Subject: Re: [gmx-users] Re: Hexagonal prism


> On Fri, 2004-02-20 at 05:11, Simon Wang wrote:
> > Hi, GMX users:
> >
> > One more question. If the box vector and angles used in GMX are the same
as
> > the conventional unit cell parameters, in the case of a hexagonal prism
(-bt
> > tric -box 5 5 3 -angles 90 90 120), the box volume should be 194.86
nm^3.
> > However, editconf report the volume as 64.95 nm^3, one third of the
previous
> > one. So I guess the box vector is not the same as the conventional unit
cell
> > parameters. But if GMX convert the hexagonal prism structure file to PDB
> > format, the box vectors show up at CRYST1 line as the unit cell
parameters.
> > I hope someone can help me out.
>
> shouldn't it be 5 x 5 x 3 sin (120) ?
>
> you are not expecting crystal symmetry, are you?
>
> >
> > Thanks,
> >
> > Simon
> >
> > >From: David van der Spoel <spoel at xray.bmc.uu.se>
> > >Reply-To: gmx-users at gromacs.org
> > >To: gmx-users at gromacs.org
> > >Subject: Re: [gmx-users] Re: [gmx-developers] Hexagonal prism
> > >Date: Thu, 19 Feb 2004 13:29:26 +0100 (CET)
> > >
> > >On Wed, 18 Feb 2004, Simon Wang wrote:
> > >
> > > >Hi, GMX users:
> > > >
> > > >I got a little bit confused about how to define a hexagonal unit cell
as
> > >a
> > > >special case of triclinic cell. When using "editconf -f conf.gro -o
> > >out.gro
> > > >-bt tric -box 5 5 3 -angles 90 90 120 -c" to assign the values of a,
b,
> > >c,
> > > ><bc, <ac, <ab, followed by conversion of "trjconv -pbc inbox -ur
compact"
> > >or
> > > >"trjconv -pbc whole -ur compact", I can get the right shape of
hexagonal
> > > >prism. But the SIZE of the hexagonal edge is about 30 angstrom, not
50 as
> > > >defined. I guess I don't fully understand the way GROMACS define the
> > > >triclinic cell. I hope someone can help me out.
> > >
> > >manual chpater 3
> > >  (with figures)
> > > >
> > > >Thanks,
> > > >
> > > >Simon
> > > >
> > > >>From: David van der Spoel <spoel at xray.bmc.uu.se>
> > > >>Reply-To: gmx-users at gromacs.org
> > > >>To: Simon Wang <sim_wang03 at hotmail.com>
> > > >>CC: gmx-users at gromacs.org
> > > >>Subject: [gmx-users] Re: [gmx-developers] Hexagonal prism
> > > >>Date: Wed, 18 Feb 2004 11:25:59 +0100 (CET)
> > > >>
> > > >>On Tue, 17 Feb 2004, Simon Wang wrote:
> > > >>
> > > >> >Hi, David:
> > > >> >
> > > >> >I've installed GROMACS 3.2.0 and tried the new version of trjconv.
> > > >> >Unfortunately I still could not get the right size of hexagonal
prism.
> > >I
> > > >> >tried the following things:
> > > >> >trjconv -pbc whole -ur compact
> > > >> >trjconv -pbc com -ur compact
> > > >> >
> > > >> >However, there is no option like "compact" for -pbc. If this is a
bug,
> > >do
> > > >> >you ever have plan to fix it in the near future?
> > > >>
> > > >>it's not necessary.
> > > >>
> > > >>trjconv -pbc inbox -ur compact does what you want.
> > > >>
> > > >>please put further questions to the mailing list only.
> > > >> >
> > > >>
> > > >>--
> > > >>David.
> >
> > _________________________________________________________________
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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