[gmx-users] No Distribution?

[Xu Dong Huang]

Should I perhaps make an edit in the index file for group 1 to be particle 1 and 2, and group 2 = particle 2 and 3? 


On Nov 2, 2013, at 6:50 PM, Xu Dong Huang <xudonghmath at gmail.com> wrote:

> @ Gromacs users,
> 
> so I did g_dist , and I’m confused by a couple of things. 1) why is it asking me for 2 groups? I have my particles of interest under 1 type, namely [ O1 ] 1    2    3, and nothing else. 2) I just picked the same group twice, and the result is gives me in xvg is the following
> There are no distances measured, that cannot be right. 
> 
>   0.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>  20.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>  40.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>  60.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>  80.0000000    0.0000000    0.0000000    0.0000000    0.0000000
> 100.0000000    0.0000000    0.0000000    0.0000000    0.0000000
> 120.0000000    0.0000000    0.0000000    0.0000000    0.0000000
> 140.0000000    0.0000000    0.0000000    0.0000000    0.0000000
> 160.0000000    0.0000000    0.0000000    0.0000000    0.0000000
> 180.0000000    0.0000000    0.0000000    0.0000000    0.0000000
> 200.0000000    0.0000000    0.0000000    0.0000000    0.0000000
> 220.0000000    0.0000000    0.0000000    0.0000000    0.0000000
> 240.0000000    0.0000000    0.0000000    0.0000000    0.0000000
> 260.0000000    0.0000000    0.0000000    0.0000000    0.0000000
> …
> 
> Thanks in advance,
> 
> Xu Huang
> 
> 
> On Nov 2, 2013, at 6:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
>> 
>> 
>> On 11/2/13 6:29 PM, Xu Dong Huang wrote:
>>> Dear All,
>>> 
>>> My martini system has 3 particles in a chain, rest is martini water, and I’m only interested in the bond length distribution of particle 1&2, 1&3 and 2&3, and I execute the following:
>>> g_bond -f npt.xtc -n index.ndx -o bonds.xvg
>>> 
>>> I get the following error:
>>> Total number of samples               : 153
>>> Mean                                  : 0.501255
>>> Standard deviation of the distribution: 0.152864
>>> Standard deviation of the mean        : 0.0123583
>>> 
>>> Back Off! I just backed up bonds.xvg to ./#bonds.xvg.1#
>>> 
>>> -------------------------------------------------------
>>> Program g_bond, VERSION 4.5.5
>>> Source code file: gmx_bond.c, line: 207
>>> 
>>> Fatal error:
>>> No distribution... (i0 = 999, i1 = 1)? ? ! ! ? !
>>> For more information and tips for troubleshooting, please check the GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>> 
>>> Upon inspecting my index files, I see that it defines my 3 particle group as:
>>> [ O1 ]
>>>   1    2    3
>>> 
>>> Then I changed the particle group index file to
>>> [ O1 ]
>>>   1    2
>>>   2	3
>>>   1	3
>>> 
>>> And I’m still getting the same error.
>>> 
>>> Any insights?
>>> 
>> 
>> Use g_dist instead and measure the distances manually.  g_analyze can then produce a distribution of those data.
>> 
>> -Justin
>> 
>> -- 
>> ==================================================
>> 
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>> 
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> 
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> 
>> ==================================================
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