[gmx-users] there are particles with all coordinates zero

[Justin Lemkul]

On 7/17/15 12:21 AM, Carlos Navarro Retamal wrote:
> Dear gmx users,
> I was analysing some trajectories (without any problem), and then just for testing, i used gmx check on them, and i got several warnings:
>
> Reading frame    3000 time 300000.000   Warning at frame 3693: there are 1 particles with all coordinates zero
> Reading frame    4000 time 400000.000   Warning at frame 4052: there are 1 particles with all coordinates zero
> Warning at frame 4079: there are 1 particles with all coordinates zero
> Warning at frame 4271: there are 1 particles with all coordinates zero
> Warning at frame 4519: there are 1 particles with all coordinates zero
> Reading frame    5000 time 500000.000   Warning at frame 5063: there are 1 particles with all coordinates zero
> Reading frame    6000 time 600000.000   Warning at frame 6766: there are 1 particles with all coordinates zero
> Reading frame    7000 time 700000.000   Warning at frame 7403: there are 1 particles with all coordinates zero
> Warning at frame 7703: there are 1 particles with all coordinates zero
> Reading frame    8000 time 800000.000   Warning at frame 8667: there are 1 particles with all coordinates zero
> Warning at frame 8682: there are 1 particles with all coordinates zero
> Reading frame    9000 time 900000.000   Warning at frame 9752: there are 1 particles with all coordinates zero
> Last frame      10000 time 1000000.000
>
> Are this warnings that ‘bad'? Should i run again my simulations? Again, just seeing them by VMD, and by making some analysis on them with several gromacs tools(trjconv, msd, rdf, etc) i didn’t see any problem, or get any error/warning message, so i really don’t know what could be the problem (or if there is one, i don’t know how to fix it).

Dump out one of those frames with trjconv and see if finding that particle is 
illustrative of anything.

In reality, I doubt this is actually a problem because it just means that you 
(infrequently) have one particle exactly at the origin.

-Justin

> Hope someone can help me,
> Best,
> Carlos
>
> ps- I tried to remove pbc conditions of the system, but i’m still getting the same error:
>
>
>
> --
> Carlos Navarro Retamal
> Bioinformatics Engineering
> Ph. D (c) Applied Sciences.
> Center of Bioinformatics and Molecular Simulations. CBSM
> University of Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 712201 798
> E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
>

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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