VMD-L Mailing List

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Mon Feb 01 2016 - 06:02:36 CST

The following command serves the purpose.

set sel1 [atomselect $mol "name H1 H2 and
sqrt(sqr(x-x1)+sqr(y-y1)+sqr(z-z1))<5 and not index $ind2"]

Regards,
Monika

On Mon, Feb 1, 2016 at 12:46 AM, Monika Madhavi <monikamadhavi_at_gmail.com>
wrote:

> Dear all,
>
> Even if I told that the atomselect command
> set sel1 [atomselect $mol "name H1 H2 and within 5 of index $ind1 and not
> index $ind2"]
>
> it does the following when I examined the output.
> The code runs without giving any errors but,
> both $ind1 and $ind2 atoms are also selected. looking for a method to get
> rid of these two atoms.
>
> Best,
> Monika
>
> On Fri, Jan 29, 2016 at 11:22 AM, Monika Madhavi <monikamadhavi_at_gmail.com>
> wrote:
>
>> Thanks everyone. This selection commands works fine for my purpose.
>> set sel1 [atomselect $mol "name HW1 HW2 and within 5 of index $ind1 and
>> not index $ind2"]
>>
>> But now I have a new question. When this atom selection is used I am
>> getting an error saying "domain error:argument not in valid range". Is this
>> an error due to pbc? How can I get rid of this?
>>
>> Thank you.
>> Best regards,
>> Monika
>>
>
>
>
> --
> W.A.Monika Madhavi
> Lecturer (Probation),
> Department of Physics,
> University of Colombo.
> 

-- 
W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.