VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed May 26 2010 - 11:26:30 CDT

On Wed, 2010-05-26 at 22:42 +0900, Hyun Tae Jung wrote:
> Hello.

hi!

> I used the "Radial Pair Distribution Function g(r)" module on VMD 1.8.7 for DPPC/DPPS mixture systems.
>
> I obtained the radial distribution function between,
> selection 1 : (type O13A or type O13B) and resname DPPS
> selection 2 : resname SOD
>
> I checked "use PBC", "display g(r)", "save to file"
>
> However, comparing the function obtained by my calculation program,
> they are different and it seems that the module is wrong.

i appreciate your courage to make a statement like this.

right now, all you can say for certain is that you get
a *different* result. which one is the correct answer
is something that will need to be determined.
so please provide some proof.

> some radial distribution functions are almost same to directly
> calculated functions, but, except above example, for instance, the
> radial distribution function between "water" and "(type O13 or type
> O14) and resname DPPS" is also wrong.

wrong in which way? what is the right answer?

cheers,
    axel.

>
> Hyun Tae Jung
>
> ===================
> Hyun Tae Jung
> Master student, Department of Chemistry
> R1214, Ricci Hall, Sogang Univ., Seoul, South Korea
> junght_at_sogang.ac.kr
>
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> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.