OK. Thank you for the kind reply.
Best regards
Vijay
On Fri, Feb 13, 2015 at 6:20 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk
> wrote:
> I have never thought of implementing more than one direction and
> apparently Dan hasn't done this either. But this is redundant
> information really because xy is simply sqrt(x^2 + y^2) and likewise
> for the other cases.
>
> Cheers,
> Hannes.
>
> On Fri, 13 Feb 2015 18:04:02 +0800
> Vijay Achari <glycoamber.gmail.com> wrote:
>
> > Thank you for the reply sir.
> >
> > By the way I would lie to ask, in the stfcdiffusion, one get the
> > output data file in the format of
> >
> > *t, x, y, z *
> >
> > If I want to get the output format like
> >
> > *t, x, y, z, xy, xz, yz, xyz* how the keywords need to be typed?
> >
> > note:
> > If I type:
> >
> > stfcdiffusion mask :10-10 time 5.0 out
> > diffusionL-maltoLyo12per-10.dat com *xy*
> >
> > I have no problem, but if I type
> >
> > stfcdiffusion mask :10-10 time 5.0 out
> > diffusionL-maltoLyo12per-10.dat com *xy xyz *
> >
> > I get error message.
> >
> > Is that possible to get* xy* and *xyz* ?
> >
> > On Fri, Feb 13, 2015 at 4:28 PM, <hannes.loeffler.stfc.ac.uk> wrote:
> >
> > > stfcdiffusion will work like the traditional diffusion command when
> > > com is not used. So this is only an additional option (the other
> > > one being that you can compute diffusion in a region defined by
> > > mask2 and lower and upper limits). Which one to choose is really a
> > > question of what you want to learn. Same goes for b).
> > >
> > > Cheers,
> > > Hannes.
> > >
> > > ________________________________________
> > > From: Vijay Achari [glycoamber.gmail.com]
> > > Sent: 13 February 2015 06:11
> > > To: AMBER Mailing List
> > > Subject: [AMBER] Water diffusion - in 2D and 3D
> > >
> > > Dear experts,
> > >
> > > I have two questions to ask.
> > >
> > > a) I tried to calculate water diffusion in hydrated bilayer system
> > > using two commands from ambertools14, *diffusion* and
> > > *stfcdiffusion.*
> > >
> > > I understand the *diffusion* command does calculate the average of
> > > movement of every atoms in a molecules frame-wise. While the
> > > *stfcdiffusion* command calculate the diffusion of center of mass
> > > (COM) of molecule's atoms in a system
> > >
> > > I wish to know which method is more appropriate to use in a
> > > reasonable way?
> > >
> > >
> > > b) In a hydrated lipid bilayer system, do we calcualte the water
> > > diffusion in 2D (x-y) or 3D (x-y-z)?
> > >
> > > Thank you.
> > > Vijay
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> > >
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> > >
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>
>
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Received on Fri Feb 13 2015 - 03:00:02 PST
