[gmx-users] About Deuterium order parameters

Poncho Arvayo Zatarain poncho_8629 at hotmail.com
Sun Nov 6 21:46:49 CET 2016

Hello gromacs user: I want to determine the deuterium order paramters for a dppc using gromacs 5.0.4 and i use the command: make_ndx -f npt.tpr -o sn1.ndx. Also i know that i need to do it too for sn2.ndx. But my question is: Should i make the index this way:

> a C34
 > a C36
 > a C37
 > a C38
 > a C50
 > del 0-21
 > q

But when i used this from C40-C50 it appears:the group is empty and wheen i use del 0-21 it appears

that i remove system, other dppc, tip3, c34, c35, c36, c37, c38, c39, c40 and group 0-9 doesn´t exist

But sn1.ndx appears. Is there anything wrong?

or should i use: >a C34|>a C35...|>a C50|>del 0-21|q ?

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