[gmx-users] Mmxcheck Messages and Timesteps

[David van der Spoel]

Shay Amram wrote:
> 
> 
> Hello Gromacs users,
> 
>  
> 
> I ran gmxcheck on a trr file I got from running energy minimization,
> 
> Gmxcheck’s output is:
> 
> ---------------------------------
> 
> */ Checking file 4PLMYWOrg01_em_tim.trr /*
> 
> */ trn version: GMX_trn_file (single precision) /*
> 
> */ Reading /* */ frame       0 time    0.000 /*
> 
> */ # Atoms  55986 /*
> 
> */ Reading frame      11 time 1001.000 /*
> 
> */ Timesteps at t=1000 don't match (100, 1) /*
> 
> */ Last frame         11 time 1001.000 /*
> 
> */   /*
> 
> */   /*
> 
> */ Item        #frames /*
> 
> */ Step            12 /*
> 
> */ Time            12 /*
> 
> */ Lambda          12 /*
> 
> */ Coords          11 /*
> 
> */ Velocities       0 /*
> 
> */ Forces           1 /*
> 
> */ Box /* */              12 /* */ /*
> 
> */   /*
> 
> */ gcq#259: "Everything Must Go" (Red Hot Chili Peppers) /*
> 
> ------------------------------------------
> 
>  
> 
> So my question is – What does that mean “Timesteps at t=1000 don’t 
> match….”?
> (and where can I find more information regarding to gmxcheck messages?)

nowehere I'm afraid. These messages are intended for MD trajectories in 
which case you usually want to have the same time step between frames. 
For EM this is meaningless.

> 
>  
> 
> Thank you in advance,
> 
> Shay Amram
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se