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

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 15 19:09:07 CET 2010

Saikat Banerjee wrote:
> Hi all,
> 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


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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