VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 18 2013 - 03:44:27 CST

On Mon, Feb 18, 2013 at 9:04 AM, Bjørnar Jensen <bje076_at_ift.uib.no> wrote:
> Hello,
>
> your selection is not complete. You're only selecting (the) parts of the
> water molecules
> that are within 10Å of index 6094. The selection you want to make is this:
>
> same resid as (waters within 10 of index 6094)

watch out. this is potentially dangerous. "resid" may not be
unique (unlike "residue" which is). it is taken as a label from
input data. in fact, it is quite common that it is not unique.

axel.

>
> I would advise you to read up on selections in the user manual.
>
>
> Best regards,
> Bjørnar.
>
>
>
> On 2013-02-18 07:56, Sindrila Dutta Banik wrote:
>>
>> Dear all,
>>
>> I have a trajectory file, which I loaded into VMD. Now want to save the
>> coordinates of waters within 10A separation from the substrate. I am able
>> to visualize to this using the following command:
>>
>> waters within 10 of index 6094
>>
>> but as soon as I am going to save this coordinates for water which are
>> with in 10A it writes few coordinate partially means one O and one H not
>> the second one. How to save the coordinates completely.
>>
>> With best regards
>> sindrila
>>
>>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.