[gmx-users] mdrun has different results with similar files

Mathieu, Jennifer J. jmathieu at mitre.org
Fri Mar 3 13:41:05 CET 2006

I've searched through your database and found many helpful suggestions,
but I am not sure why mdrun successfully runs on some files but not
others.  The protein files are pretty but I get the following results
when running mdrun.  (Yesterday I tried attaching the files but they
made the email too big and it got returned)
ABPa1OUT.pdb fails (Number of grid cells is zero. Probably the system
and box collapsed.)
QBPq1OUT.pdb succeeds with errors (some bonds rotated more than 30
GBPg1OUT.pdb succeeds
Also, the topology files for ABP and GBP are made using 1 file, while
the QBP topology file is made using 2 files.  (when 2 files are used, I
edit the topol.top file to have the posre_A.itp and posre_B.itp files
-- #include "posre_A.itp")
Here are the commands I'm running:
pdb2gmx -f file_name.pdb -o -p < input.txt
editconf -bt octahedron -f -o -c -d 0.7
genbox -cp conf.gro -cs -o -p
grompp -f -c out.gro -p -o
mdrun -s -o -c -g -e
Thank you,
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