[gmx-users] No Distribution?

[Justin Lemkul]

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

-- 
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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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