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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Received on Fri Feb 13 2015 - 02:30:03 PST
