[gmx-users] grompp not recognizing mdp file parameters

[David van der Spoel]

toma0052 wrote:
> Hello,
>      It seems that I am having a problem in that grompp is not recognizing
> the parameters that I enter into an mdp file, nor is it recognizing the text
> in the .top file.  When I run a simulation, the output that I get is as
> follows:
> 
> ERROR: invalid enum 'md' for variable integrator, using 'md'
> Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'
> ERROR: invalid enum 'grid' for variable ns-type, using 'Grid'
> Next time use one of: 'Grid' 'Simple'
> ERROR: invalid enum 'xyz' for variable pbc, using 'xyz'
> Next time use one of: 'xyz' 'no' 'full'
> ERROR: invalid enum 'PME' for variable coulombtype, using 'Cut-off'
> Next time use one of: 'Cut-off' 'Reaction-Field' 'Generalized-Reaction-Field'
> 'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift' 'User' 'Generalized-Born'
> 'Reaction-Field-nec' 'Encad-shift' 'PME-User'
> ERROR: invalid enum 'yes' for variable optimize_fft, using 'no'
> Next time use one of: 'no' 'yes'
> ERROR: invalid enum 'berendsen' for variable tcoupl, using 'No'
> Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen'
> 'Andersen-interval'
> ERROR: invalid enum 'berendsen' for variable Pcoupl, using 'No'
> Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic'
> ERROR: invalid enum 'Semiisotropic' for variable Pcoupltype, using
> 'Isotropic'
> Next time use one of: 'Isotropic' 'Semiisotropic' 'Anisotropic'
> 'Surface-Tension'
> ERROR: invalid enum 'all-bonds' for variable constraints, using 'none'
> Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'
> checking input for internal consistency...
> sh: /lib/cpp: No such file or directory
> processing coordinates...
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: grompp.c, line: 448
> 
> Fatal error:
> number of coordinates in coordinate file (area_1.03_1.gro, 17365)
>              does not match topology (dppc.top, 0)
> -------------------------------------------------------
> 
>      What could be the problem here?  Is this just some simple formatting
> error that I've missed?  I have run simulations before, and everything seemed
> to work out fine.  The run above is simply the same files from the successful
> simulation copied into a new directory with a few alterations made to the mdp
> file.  If my other files still run, why are essentially the same files not
> recognized when put into a new directory?
> 

maybe you have a DOS formatted file? try dos2unix or something like that.

what platform are you running on?


-- 
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