Justin A. Lemkul wrote:
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
Actually there were a bunch more improvements that I'd made which hadn't
been correctly added to CVS. Erik's fixed that now. Road-testing would
be welcome. There aren't any more bd-temp issues, and he seems to have
taken up your suggestion below also.
Mark
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:
355c355
< 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
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