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

[Justin Lemkul]

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.


-Justin


On Wednesday, March 8, 2017 5:31 PM, Justin Lemkul  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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Use of -nr for order parameters

[Wally Davis]

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? 

On Wednesday, March 8, 2017 5:31 PM, Justin Lemkul  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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
-- 
Gromacs Users mailing list

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

[Justin Lemkul]

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

[Wally Davis]

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?
-- 
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