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 frame3000 time 30.000 Warning at frame 3693: there are 1
particles with all coordinates zero
Reading frame4000 time 40.000 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 frame5000 time 50.000 Warning at frame 5063: there are 1
particles with all coordinates zero
Reading frame6000 time 60.000 Warning at frame 6766: there are 1
particles with all coordinates zero
Reading frame7000 time 70.000 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 frame8000 time 80.000 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 frame9000 time 90.000 Warning at frame 9752: there are 1
particles with all coordinates zero
Last frame 1 time 100.000
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.navarr...@gmail.com or cnava...@utalca.cl
--
==
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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