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

[Carlos Navarro Retamal]

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).
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