Tutorial-l Mailing List

From: Timothy Isgro (timisgro_at_ks.uiuc.edu)
Date: Fri Feb 16 2007 - 11:45:31 CST

Hello Won-Young,

 From the VMD User's Guide, gofr usage:
- gofr selection1 selection2 [delta value] [rmax value] [usepbc
boolean] [selupdate boolean] [first value] [last value] [step value]

The problem is that your "selections" are invalid. Selection1 and
selection2 refer to VMD atomselections specifically, which must be
defined as follows:
[atomselect <molecule id> <atomic selection>]

Your problem will be solved by invoking the following commands:

> set mysel1 [atomselect top "type CA"]
> set mysel2 [atomselect top "type O"]
> measure gofr $mysel1 $mysel2

This will set 2 variables, one which stores the atomselection for all
atoms of type CA, and one for type O. Then, the pair distribution
function will be calculated.

-Tim

On Feb 6, 2007, at 6:21 PM, <wahn_at_uiuc.edu> <wahn_at_uiuc.edu> wrote:

> Dear VMD users,
>
> I tried to calculate gofr between calcium and oxygen.
>
> In the tcl window, I typed the following command.
>
> measure gofr {type CA} {type O}
>
> This returned me that the first selection is invalid.
> What is wrong in my expression?
>
> Thanks for your help in advance.
>
> Won-Young
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