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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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Feb 13 2015 - 02:30:04 PST
