[gmx-users] RV: About Deuterium order parameters

Justin Lemkul jalemkul at vt.edu
Tue Nov 8 02:36:13 CET 2016

On 11/6/16 10:13 PM, Poncho Arvayo Zatarain wrote:
> Hello gromacs users: 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?

An empty group means your selection matches nothing.  Probably your atoms are 
named differently.  Beware copying directly from a tutorial and hoping it will 
work for everything.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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