[gmx-users] Use of -nr for order parameters

Justin Lemkul jalemkul at vt.edu
Fri Mar 10 02:16:50 CET 2017

On 3/9/17 2:41 PM, Wally Davis wrote:
> My input line is:
> gmx order -s test.tpr -f fullTraj.trr -n orderParam.ndx
> The index file is formated with 3 groups, one per carbon along the chain of interest.
> The error I get is: "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"
> Every example I have seen online does not include an nr option. Any ideas on what this is or how to get rid of the error?

The index file passed to -nr is only for radial axis calculations, invoked via 
the -radial option.  This shouldn't be possible with the command given above.


>     On Wednesday, March 8, 2017 5:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 3/8/17 4:46 PM, Wally Davis wrote:
>> Hi,
>> I'm trying to use the g_order function. I have formated my .ndx file with one group per carbon and provide this file under the -n input option. However, I alway get the error that the -nr file is not found. What is the extra .ndx file I need to provide?
> Please provide your full command and all relevant screen output, including the
> error.
> -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


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