[gmx-users] grompp error with cpp

David van der Spoel spoel at xray.bmc.uu.se
Sat Mar 24 08:52:42 CET 2007

toma0052 wrote:
> Hello,
>      I just installed Gromacs on my windows machine under cygwin, and
> everything seemed to go fine with the installation and whatnot.  Initially,
> when I tried to run a simulation, I obtained the error that Gromacs found the
> number of coordinates in my .top file to be 0, because it could not find the
> cpp.  From the mailing list archives, I gathered that Gromacs was checking
> for cpp in /lib/cpp whereas in cygwin the cpp is in /bin/cpp.  So, as in the
> post, I created a link in /lib pointing to /bin/cpp.  I ran a simulation, and
> everything went fine.  Now, I am trying to run another simulation, and I am
> running into the same problem as before.  When I execute grompp, I get this
> error:
> Back Off! I just backed up md_shear_run.mdp to ./#md_shear_run.mdp.2#
> checking input for internal consistency...
> ...ling /lib/cpp
> : No such file or directory
> cpp exit code: 32512

replace /lib/cpp with /bin/cpp (with or without .exe) in the mdp file

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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