[gmx-users] Analysis of CNT in water solution

[Christopher Stiles]

Thank you very much as always you're a great help BOB! I have about 4 hours
till my next simulation finishes so I will let you know how it works then.

~Christopher Stiles
College of Nanoscale Science and Engineering (CNSE)
State University of New York, Albany, New York 12203, USA

>-----Original Message-----
>From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
>On Behalf Of Robert Johnson
>Sent: Monday, August 06, 2007 11:11 AM
>To: Discussion list for GROMACS users
>Subject: Re: [gmx-users] Analysis of CNT in water solution
>
>The best and easiest way to do this would be to write a script within
>VMD. You can define an atom selection something like:
>set wat_inside [atomselect $mol_id "same residue as water and (z >
>$NT_beg and z < $NT_end and sqrt((x-$x_NT)*(x-$x_NT) +
>(y-$y_NT)*(y-$y_NT)) < $NT_radius)]
>
>Here $mol_id is the molecule id of your system (probably 0), $NT_beg
>and $NT_end are the beginning and ending coordinates (in the
>z-direction) of your nanotube, $x_NT and $y_NT are the x and y
>coordinates of the nanotube center, and $NT_radius is the nanotube
>radius.
>
>Then you can loop over the frames in your trajectory and update that
>atom selection with the commands:
>$wat_inside frame $n
>$wat_insde update
>
>Then you can figure out how many water molecules are within your nanotube
>by
>$wat_inside num
>
>Bob
>
>
>On 8/5/07, Christopher Stiles <CS145331 at albany.edu> wrote:
>>
>>
>>
>>
>> I am trying to look at the # of water molecules within the CNT as a
>function
>> of time and I was wondering if there was another app like Trjorder that
>> maybe instead of using a group of molecules as the reference you could
>use
>> coordinates i.e. the axis of the CNT, or if there is a better way to go
>> about this?
>>
>>
>>
>> Information on the setup; it is a 2.81700   2.81700   3.35410 box with a
>( 6
>> , 6 ) CNT (centered in the box) and 811 spc216 molecules and it is at
>300k
>> and run for 200ps.
>>
>>
>>
>> Thank you for help,
>>
>> ~Christopher Stiles
>>
>> College of Nanoscale Science and Engineering (CNSE)
>>
>> State University of New York, Albany, New York 12203, USA
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