VMD-L Mailing List

From: Emily Moore (emily.moore_at_utah.edu)
Date: Tue Aug 19 2008 - 14:23:29 CDT

Thanks for the help. I was afraid that was the case. I'm aware of the gofr
issues and I'm using the alpha test build for my calculations.

Thanks again,
Emily Moore

On 8/19/08 12:06 PM, "Axel Kohlmeyer" <akohlmey_at_cmm.chem.upenn.edu> wrote:

> On Tue, 19 Aug 2008, Emily Moore wrote:
>
> EM> Hello,
>
> hello emily,
>
> EM> Iım trying to calculate the gofr for multiple frames of a trajectory. For
> EM> each frame, I would like to have the gofr for atoms ³type 4² against ³type
> EM> 4², with the atoms that are considered to have a type=4 updated every
> frame.
>
> please note that VMD does the assignment of atom types only for the
> first frame of a trajectory. that frame is always read, even if you
> discard the coordinates from it. to have properties that change over time
> stored on a per-atom, per-timestep basis, you have to write some scripting
> to read in that data and store it in one of the user fields. see, e.g.,
>
> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part4.html#cha
> p6_sect4
>
> EM> The code below does the first frame correctly, but does not seem to update
> EM> the current frames type =4 atoms when calculating for the later frames.
> Iıve
> EM> tried using ³$sel1 update² and ³$sel1 frame $i² and Iıve tried taking out
> EM> ³mol delete top² and ³$sel1 delete² but it still updates incorrectly, or
> not
> EM> at all (Iım not sure which is the problem, probably not updating at all).
> EM> Also, if there is any way to do this without a tcl script, within the
> EM> measuring gofr options window, that would be nice to know.
>
> if you store the relevant information in the user field, yes.
> i'm currently working on a project with similar problems and
> can hopefully contribute a more specific example to the gofr
> documentation soon.
>
> please note, that we recently discovered and fixed(!) a few
> (minor) bugs in the gofr code so that using an alpha test
> build of VMD 1.8.7 is highly recommended. see
> http://www.ks.uiuc.edu/Research/vmd/alpha/
>
> cheers,
> axel.
>
> EM> Thanks,
> EM> Emily
> EM>