[gmx-users] Re: Re: Re: g_velacc problem (Florian Dommert)

[Florian Dommert]

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On 10/15/2010 01:09 AM, Eudes Fileti wrote:
> Dear Florian, thanks again.
> I have worked with confined systems, where motion 
> in a given direction/plane is preferred. The accuracy of the MSD 
> approach for calculating the diffusion coefficient has been 
> questioned for this my system. So I need to calculate 
> D via VACF. Considering my limited abilities to programming 
> I wonder if it would be possible to you send me more 
> details about the changes that I should implement the program. 
> 
> Any help will be very useful!

As I mentioned, in my opinion you just have to insert an if statement,
when adding the z-direction of the velocity to the VACF. I will take a
look at it at ASAP and report back.

Cheers,

Flo


> Bests
> eef
> _______________________________________
> Eudes Eterno Fileti
> Física da Matéria Condensada
> Simulação Computacional de Nano-estruturas via Dinâmica Molecular
> 
> 
> 
> 
>     Message: 1
>     Date: Thu, 14 Oct 2010 17:22:38 +0200
>     From: Florian Dommert <dommert at icp.uni-stuttgart.de
>     <mailto:dommert at icp.uni-stuttgart.de>>
>     Subject: Re: [gmx-users] Re: g_velacc problem (Florian Dommert)
>     To: Discussion list for GROMACS users <gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>>
>     Message-ID: <4CB7203E.1020307 at icp.uni-stuttgart.de
>     <mailto:4CB7203E.1020307 at icp.uni-stuttgart.de>>
>     Content-Type: text/plain; charset=ISO-8859-1
> 
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> 
>     On 10/14/2010 04:41 PM, Eudes Fileti wrote:
>     > Dear Florian, thanks for the help. I wonder just one more thing.
>     > Is it possible to obtain the lateral diffusion coefficient in a
>     specific
>     > plane (say xy)
>     > using g_velacc? Or it is only possible with g_msd?
> 
>     I am not sure, but the MSD is nothing else than the integrated VACF, so
>     if you modify the code correspondingly it should work. The modification
>     shouldn't be that hard, because you just have to prevent summing up a
>     certain direction of the velocity.
> 
>     /Flo
> 
>     > Bests
>     > eef
>     > _______________________________________
>     > Eudes Eterno Fileti
>     > Física da Matéria Condensada
>     > Simulação Computacional de Nano-estruturas via Dinâmica Molecular
>     >
>     >
>     >
>     >
> 
> 
>     - --
>     Florian Dommert
>     Dipl.-Phys.
> 
>     Institute for Computational Physics
> 
>     University Stuttgart
> 
>     Pfaffenwaldring 27
>     70569 Stuttgart
> 
>     Phone: +49(0)711/685-6-3613
>     Fax:   +49-(0)711/685-6-3658
> 
>     EMail: dommert at icp.uni-stuttgart.de
>     <mailto:dommert at icp.uni-stuttgart.de>
>     Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
> 
> 


- -- 
Florian Dommert
Dipl.-Phys.

Institute for Computational Physics

University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Phone: +49(0)711/685-6-3613
Fax:   +49-(0)711/685-6-3658

EMail: dommert at icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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