[gmx-users] Help!

[David]

On Fri, 2004-02-20 at 09:15, Ankur wrote:
> 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.
> 
trjorder
g_msd

> 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.
> > >
> > > _________________________________________________________________
> > > Get fast, reliable access with MSN 9 Dial-up. Click here for Special
> Offer!
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> > >
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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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> 
> 
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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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