[gmx-users] Re: g_hydorder

Nidhi Katyal nidhikatyal1989 at gmail.com
Tue Oct 8 11:28:06 CEST 2013

First I created index file with all oxygen atoms of water molecules using
make_ndx -f lys_full.gro -o index_soloxy.ndx
Then I used g_hydorder -f lys_full.xtc -s lys_full.tpr -n index_soloxy.ndx
-or file1.out file2.out

Following output appeared:
Program g_hydorder, VERSION 4.6.3
Source code file: /root/gromacs-4.6.3/src/tools/gmx_hydorder.c, line: 702

Fatal error:
No or not correct number (2) of output-files: 1
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Please guide me in filing redmine issue. I have read following link:

But could not locate link to file redine issue.

On Wed, Oct 2, 2013 at 12:41 AM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

> On 2013-10-01 19:51, Nidhi Katyal wrote:
>> Please provide me with necessary guidance. I have already posted this
>> thrice but have not got a single reply
>> Thanks in advance.
>> On Tue, Oct 1, 2013 at 3:40 PM, Nidhi Katyal <nidhikatyal1989 at gmail.com>*
>> *wrote:
>>  Hello everyone,
>>> I would like to calculate angle tetrahedral order parameter of water
>>> molecules as defined by  Chau et al (eq 3). I am using g_hydorder of
>>> gromacs 4.6.3 with my index group containing all oxygen atoms of water:
>>> g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out
>>> file_2.out -n index.ndx
>>> I am getting following error;
>>> No or not correct number (2) of output files :1
> Please give exact command line with file names and output cut-and pasted.
> The program needs indeed two output files of both types.
> It seems that your command line is ok nevertheless.
> Please file a redmine issue and assign it to me.
>  It seems from above that correct number should be 2 but user is supplying
>>> only 1 and so is the error. But I am giving names of two output files.
>>> Also, I am unable to understand what exactly is contained in these
>>> two/four output files. I tried to comprehend this by looking at
>>> gmx_hydorder.c and could make a guess that I actually need sgmol/sgmean
>>> (variables as defined in program) as the final output.
>>> Please help me understand the usage of this command in order to fulfill
>>> my
>>> aim.I have posted this twice but have not got a single reply.
>>> Thanks in advance.
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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