[gmx-users] Lingering problems with the test set

Justin A. Lemkul jalemkul at vt.edu
Mon May 25 16:20:43 CEST 2009

Hi All,

I just grabbed the latest version of the test set from CVS, noting the updates 
and improvements to the package.  I ran gmxtest.pl, and all simple, complex, and 
kernel tests passed, but pdb2gmx failed.  Looking into the pdb2gmx.log file, 
grompp complains about "Unknown or double left-hand 'bd-temp' in parameter 
file."  Commenting this line out in the em.mdp file circumvents the problem, but 
leads to multiple failures of the ffoplsaa+tip4p/tip5p (-vsite none) tests 
involving the 1pga.pdb structure.  The problem is naming inconsistency between 
MW-HW3 in the case of tip4p, and LP1/LP2-HW3/HW4 in the case of tip5p.  Of 
course, these errors come from pdb2gmx processing of the crystal waters and use 
of the hydrogen database.

To circumvent all of these problems in one move, I made the following change to 
the gmxtest.pl script:

< 		    open(PIPE,"$grompp -f ../../../../em -c b4em 2>&1 |");
 > 		    open(PIPE,"$grompp -maxwarn 10 -f ../../../../em -c b4em 2>&1 |");

Perhaps this change would be appropriate for the general public as well.  With 
this modification, every test passes as expected, since grompp will correctly 
use the names from the topology.

It might also be appropriate to kill the bd-temp line in em.mdp, since this is 
not a valid .mdp option any more :)



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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