[gmx-users] Error in deuterium order parameters, index, nr

[Justin Lemkul]

On 6/8/17 10:47 AM, Poncho Arvayo Zatarain wrote:
> 
> 
> Hello gromacs users: i´m trying to graph my xvg of deuterium order parameters with the command: gmx order -s file.tpr -f fiile.xtc -n sn1.ndx -d z -od deuter_sn1.xvg but the following error appears: Error in user input: Invalid input lines in option nr. Required option was not provided and the default file "index" does not exist or is not accessible. The following extensions were tried to complete the file name: .ndx.
> Before that, to generate .ndx file i use the command: gmx make_ndx -f file.tpr -o sn1.ndx. What can i do to solve this? What is option nr? is necessary to use it?
> 

The error is saying that the -nr option is looking for a file called index.ndx 
but that doesn't exist.

-nr should only be used in the case of radial calculations; it seems older 
versions incorrectly listed it as a mandatory argument rather than an optional 
one.  Upgrade to the latest GROMACS and try again.

-Justin

-- 
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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

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