[gmx-users] gromacs under cygwin

Claudio J. Margulis claudio-margulis at uiowa.edu
Sat Aug 16 17:33:00 CEST 2003

I already had the link, it's something else.
pdb2gmx core dumps.
I just did it all over again, make clean, make, make install,
and it compiles no problem, but if I try pdb2gmx for example
it still core dumps.

The only non standard thing
was changing fmax for gmx_fmax as Erik suggested in

this is when you run grompp on the water example
      -load string         Releative load capacity of each node on a 
                            machine. Be sure to use quotes around the 
                            which should contain a number for each node
    -maxwarn    int     10  Number of warnings after which input processing
-[no]check14   bool     no  Remove 1-4 interactions without Van der Waals

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Cleaning up temporary file grompp002200
Fatal error: Bonded/nonbonded atom type 'ðúw`8õwÿÿÿÿã9ùwrÝw1' not found!
here is pdb2gmx -f spc216.pdb -o tmp.gro

     -dist   real    0.3  Maximum donor-acceptor distance for a H-bond (nm)
    -[no]una   bool     no  Select aromatic rings with united CH atoms on
                            Phenylalanine, Tryptophane and Tyrosine
    -[no]H14   bool     no  Use 1-4 interactions between hydrogen atoms
   -[no]ignh   bool     no  Ignore hydrogen atoms that are in the pdb file
-[no]missing   bool     no  Continue when atoms are missing, dangerous
    -posrefc   real   1000  Force constant for position restraints
      -dummy   enum   none  Convert atoms to dummy atoms: none, hydrogens or
 -[no]heavyh   bool     no  Make hydrogen atoms heavy
-[no]deuterate bool     no  Change the mass of hydrogens to 2 amu

Reading spc216.pdb...
Segmentation fault (core dumped)

Saludos a la gente de la Plata.


in my own cygwin installation the cpp preprocesor is located in /bin/cpp
rather than /lib/cpp
create a link in /lib/ pointing to /bin/cpp so usual mdp files will run ok.
cd /bin
ln /lib/cpp.exe
Diego Vallejo  -  vallejo at iflysib.unlp.edu.ar  ++++++++++++++++++++++
Instituto de Física de Líquidos y Sistemas Biológicos  - UNLP/CONICET
59 Nº789  (B1900BTE) La Plata.                                      +
Tel: +54 221 425 4904/ 423 3283  #17    Fax: +54 221 425 7317       +

Claudio J. Margulis
Assistant Professor
Department of Chemistry
University of Iowa
Iowa City, IA 52242

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