VMD-L Mailing List

From: Bjørnar Jensen (bje076_at_ift.uib.no)
Date: Mon Feb 18 2013 - 04:27:33 CST

Thanks for the feedback.

I've been blessed by unique resids from the simulation software I've used,
thus not experienced the potential short coming of this selection.
I noticed your note on using "fragment", and clearly it is the safer
choice.

I advise myself to read up on selections in the user manual ;)

Best regards,
Bjørnar.

On 2013-02-18 10:44, Axel Kohlmeyer wrote:
> 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
>>>
>>>
>
>