[gmx-users] Re: g_hydorder

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 1 21:11:38 CEST 2013

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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