VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Sep 19 2011 - 06:51:38 CDT

On Sun, 2011-09-18 at 22:37 -0700, hamid mosaddeghi wrote:
> Dear User of VMD
>
>
> I used hydrogen bond option for calculate hbond but this code have
> problem. after compare output data with other software , as said
> before in vmd topic,
>
> I think that this code don't work correct. whole data that reach from
> vmd if multiply in a factor , data become correct. then in source of
> hbond code need this
> factor.

this is a completely pointless statement.

please provide _proof_, i.e. explicit test examples
that show the hydrogen bond calculation does not work
as documented. just claiming, that you don't get different
numbers with different programs, doesn't mean zip.
there are several ways to define what a hydrogen bond
is and there are different ways to sum them up.
how do we know that you didn't mess up?

using a fudge factor is a _very bad_ approach. either
VMD does the correct calculation or not. a fudge factor
doesn't make a bad calculation correct.

axel.

>
> Hamid Mosaddeghi
>
> Phd Student Of Computational Chemistry
>
> Best Regards