VMD-L Mailing List

From: fariba taghavi (faribataghavifariba_at_gmail.com)
Date: Sat Jun 30 2012 - 10:36:44 CDT

Dear Meisam and Albert,
You just need to write a short script to select the oxegen atoms is
an specific geometry and update this selection every step. Then, count the
number of your selections in each step. Now, you have number of oxygen
atoms in your interested hole foe each step.
Good Luck,
fariba

On Thu, Jun 28, 2012 at 4:48 PM, Albert <mailmd2011_at_gmail.com> wrote:

> yes, it would be very nice if Fariba can talk a little bit more on such
> scripts.
>
>
> thank you very much
> Albert
>
> On 06/28/2012 12:38 PM, meisam valizadeh kiamahalleh wrote:
>
> Dear Fariba
> Glad to hear your helpful reply on this matter. May I know if you have any
> TCl script for calculating the water molecule's number over the simulation
> time and a distance from the surface? I guess the suggestion that you made
> here is for finding the number of water molecule at a specific time, if I
> am not mistaken.
> I would be very grateful if you could share your experience with us.
> Cheers,
> Meisam
>
> On Thu, Jun 28, 2012 at 3:39 PM, fariba taghavi <
> faribataghavifariba_at_gmail.com> wrote:
>
>> Dear Albert,
>> Actually you can not find this option directly in the VMD but, you can
>> use TLC to write a short code. My suggestion is to select oxygen atom
>> in the hole (for example by "atomselect" to choose oxygen atoms with
>> x^2+y^2+Z^2<=16, it is related to the shape of the hole) and then you
>> can get the number of your selected atoms.
>>
>> Good Luck,
>> Fariba Taghavi
>> PhD Candidate in Physical Chemistry
>> Tarbiat Modares University
>>
>> On 6/27/12, Albert <mailmd2011_at_gmail.com> wrote:
>> > hello:
>> >
>> > I've finished a MD and I would like to to make statistics for the
>> > water density in the 'hole' within the protein at specific region. I am
>> > wondering, is it possible for VMD to do so ? Does anybody have any
>> > suggestions? I've searched in the mailist and VMD plug-in/scripts pages,
>> > but didn't find anything related.
>> >
>> > thank you very much
>> > Albert
>> >
>>
>
>
>
>