v3.3 beta errors was [gmx-users] Scaling on SGI Altix 3700 Bx2

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Tue Jul 5 00:47:53 CEST 2005

Hey Berk,

> >This is the error that grompp throws up if I use the -e flag.
> >-------------------------------------------------------
> >Program grompp, VERSION 3.3_beta_20050202
> >Source code file: enxio.c, line: 358
> >
> >Fatal error:
> >Could not find energy term named 'Pcoupl-Mu-XX'
> >-------------------------------------------------------
> Are you really sure you did everything the same as before?
> This seems like you are trying to continue a run with an mdp 
> with pressure coupling from a run without pressure coupling. 
> You can just leave out the -e flag.

I tried it with the -e flag to see if it could fix the following mdrun
error, which occurs with or without that in grompp.  I am not worried
about this, just provided as thought may provide more assistance with
the following error.

> >And this is what mdrun gives.
> >-------------------------------------------------------
> >Program mdrun, VERSION 3.3_beta_20050202
> >Source code file: nsgrid.c, line: 220
> >
> >Fatal error:
> >Number of grid cells is zero. Probably the system and box collapsed.
> >
> >-------------------------------------------------------

> When does it give this?
> At step 0?

I believe so.  This comes after it says "starting mdrun" then on the
next line it lists the number of steps the sim is to be run for and the
simulation time, then comes out the above error, a line of the "quotes",
"halting program mdrun" then some MPI errors .....

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9073
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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