[gmx-users] How to select the molecules within a defined radius

[Saikat Banerjee]

>
>
> Saikat Banerjee wrote:


>> I am doing some simulations in binary solvent water and DMSO using ffG43a6
>> forcefield. I need to calculate the composition fluctuation of the solvent.
>> I have done that with hand-written codes using the trajectory files
>> generated by GROMACS. I selected a sphere at a fixed center and noted the
>> number of water and DMSO molecules within that cut-off. I would like to know
>> if there are any methods to do the same within GROMACS.
>>
>
> Have a look at:
>
> g_dist -dist
>
> -Justin
>
> Thanks for your reply. It could have been done with g_dist -dist or
trjorder -r. But the problem here is a bit different. I wanted to compute
the number of molecules within a cut-off from the center of the box, and not
from the center of mass of another atom.  So, the problem can be re-framed
as - is there any way to fix a dummy massless atom at the box centre ?





> Thanking you,
>>
>> Saikat
>>
>> --
>> -------------------------------------------------------------------
>> Saikat Banerjee
>> Integrated Ph.D student
>> Prof B. Bagchi's group
>> Room no. 210
>> Solid State and Structural Chemistry Unit (SSCU)
>> Indian Institute of Science
>> Bangalore-560012
>> -------------------------------------------------------------------
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
>
>
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