[gmx-users] No Distribution?

[Xu Dong Huang]

@ Justin,

Thanks. I fixed the index files like you suggested. I’m getting logical results now. 

All the best,

On Nov 2, 2013, at 7:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 
> 
> On 11/2/13 7:01 PM, Xu Dong Huang wrote:
>> 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?
>> 
> 
> No.  If you want three different distances, you need three groups, as I said in my previous message, and I even wrote the exact index file for you.
> 
> -Justin
> 
>> 
>> 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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>>> 
>> 
> 
> -- 
> ==================================================
> 
> 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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