[gmx-users] Tetrahedral order

[Justin Lemkul]

On 7/9/19 4:24 AM, Omkar Singh wrote:
> Dear all,
> I want to calculate the Tetrahedral order parameter through gmx. Can anyone
> help? Eventhough I tried but my system has 500 water molecules Fir that I
> am unable to make index file because it will take lots of time for typing
> any suggestions. Commend
> gmx order -f .xtc -s .tpr -b 0 -e 10000 -n .ndx -nr .ndx  -d y -permolecule

You're using the wrong tool. gmx order is explicitly for carbon atoms, 
e.g. alkyl chains in phospholipids. You want gmx hydorder.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================