[gmx-users] Compute the end to end distance distribution for surfactant

Justin Lemkul jalemkul at vt.edu
Thu Jan 10 12:41:43 CET 2013

On 1/10/13 6:38 AM, ABEL Stephane 175950 wrote:
> Dear All,
> I would like to compute the end to end distribution for different parts (i.e.  hydrophobic and the polar) of several detergent molecules. I know that g_polystat can do the job and indeed i can obtain the end-to-end distance of the whole  molecule (at least for  the distance vs. time). But it is not clear to me how to obtain the end to end distance values for the different parts of my molecule with g_polystat.

g_polystat -h includes:

"The end-to-end distance is then determined using the first and the
last atom in the index group for each molecules."

As with nearly all Gromacs programs, you can give it an index file of whatever 
subset of atoms you want.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list