[gmx-users] gmx order has no output

[Justin Lemkul]

On 2/21/17 3:17 AM, Мижээ Батсайхан wrote:
> Dear gmx users,
>
> I run heterogeneous membrane simulation which consists of several different
> type of lipids. Now I would like to analysis of order parameters.
> I used following command for sn-2 order parameters.
>
> gmx order -s ../step7_1.tpr -f ../nopbc.xtc -n sn2.ndx -od deuter_sn2.xvg
> -o order-sn2.xvg -d z -nr ../index.ndx
>
> in the result file, only header rows printed, and there is no data as
> following
>
> *****************************************
>  # Created by:
> #                    :-) GROMACS - gmx order, VERSION 5.1 (-:
> #
> # Executable:   /usr/local/gromacs/5.1.0/bin/gmx
> # Data prefix:  /usr/local/gromacs/5.1.0
> # Command line:
> #   gmx order -s ../step7_1.tpr -f ../nopbc.xtc -n sn2.ndx -od
> deuter_sn2.xvg -o order-sn2.xvg -d z -nr ../index.ndx
> # gmx order is part of G R O M A C S:
> #
> # Green Red Orange Magenta Azure Cyan Skyblue
> #
> @    title "Order tensor diagonal elements"
> @    xaxis  label "Atom"
> @    yaxis  label "S"
> @TYPE xy
>
> *****************************************
> Do you have an explain and any suggests, please?
>

Looks like the command probably failed.  Check the screen output of gmx order 
for any error messages.  Make sure your index groups are lipid-specific; you 
can't analyze multiple lipid types at once in this analysis.

-Justin

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

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
http://mackerell.umaryland.edu/~jalemkul

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