[gmx-users] No Distribution?

[Justin Lemkul]

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

==================================================