[gmx-users] Many failed tests in gromacs 4.6.3 installation

[Herbert Georg]

Hi there,

I have installed a couple of days ago the latest (4.6.3) version of 
Gromacs, in a 12-core Xeon machine using the latest version (14.0) of 
the non-comercial Intel C++ compiler for linux.

The installation seems to have succeeded, but I ran the latest set of 
tests available (4.6.1) and most of the tests PASSED, but still many of 
them FAILED.

I've checked the tests that failed, and all of them are related to the 
grompp. Performing a <grep "FAILED"> in the output of the <./gmxtest.pl 
all> command gives the following:

--------------------------------
hcgeorg at araguaia:~/source/regressiontests-4.6.1> grep "FAILED" tests.log
FAILED. Check grompp.out files in nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1
FAILED. Check grompp.out files in nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1
FAILED. Check grompp.out files in nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3
FAILED. Check grompp.out files in nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4
FAILED. Check grompp.out files in nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1
FAILED. Check grompp.out files in nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1
FAILED. Check grompp.out files in nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3
FAILED. Check grompp.out files in nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4
FAILED. Check grompp.out files in nb_kernel_ElecEwSh_VdwNone_GeomW3P1
FAILED. Check grompp.out files in nb_kernel_ElecEwSh_VdwNone_GeomW4P1
FAILED. Check grompp.out files in nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1
FAILED. Check grompp.out files in nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1
FAILED. Check grompp.out files in nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3
FAILED. Check grompp.out files in nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4
FAILED. Check grompp.out files in nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1
FAILED. Check grompp.out files in nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1
FAILED. Check grompp.out files in nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3
FAILED. Check grompp.out files in nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4
FAILED. Check grompp.out files in nb_kernel_ElecEwSw_VdwNone_GeomW3P1
FAILED. Check grompp.out files in nb_kernel_ElecEwSw_VdwNone_GeomW4P1
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1
FAILED. Check grompp.out files in nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4
38 out of 142 kernel tests FAILED
FAILED. Check grompp.out files in coulandvdwtogether
FAILED. Check grompp.out files in expanded
2 out of 9 freeenergy tests FAILED
--------------------------------------------------------

Now, looking at the grompp.out files (or in the grompp.warn file), they 
all seem to have more then the 2 warnings that are in the reference.warn 
file. For instance:

---------------------------------------------------------
hcgeorg at araguaia:~/source/regressiontests-4.6.1> cat 
kernel/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1/grompp.warn
WARNING 1 [file topol.top, line 103]:
   The bond in molecule-type Protein between atoms 1 N and 2 H1 has an
   estimated oscillational period of 1.0e-02 ps, which is less than 5 times
   the time step of 2.0e-03 ps.
   Maybe you forgot to change the constraints mdp option.

WARNING 2 [file grompp.mdp]:
   Can not exclude the lattice Coulomb energy between energy groups

WARNING 3 [file grompp.mdp]:
   The sum of the two largest charge group radii (0.077669) is larger than
   rlist (0.900000) - rvdw (0.900000).
   With exact cut-offs, better performance can be obtained with
   cutoff-scheme = Verlet, because it does not use charge groups at all.

WARNING 4 [file grompp.mdp]:
   The sum of the two largest charge group radii (0.168825) is larger than
   rlist (0.900000) - rcoulomb (0.900000).
   With exact cut-offs, better performance can be obtained with
   cutoff-scheme = Verlet, because it does not use charge groups at all.

hcgeorg at araguaia:~/source/regressiontests-4.6.1> cat 
kernel/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1/reference.warn
WARNING 1 [file topol.top, line 103]:
   The bond in molecule-type Protein between atoms 1 N and 2 H1 has an
   estimated oscillational period of 1.0e-02 ps, which is less than 5 times
   the time step of 2.0e-03 ps.
   Maybe you forgot to change the constraints mdp option.

WARNING 2 [file grompp.mdp]:
   Can not exclude the lattice Coulomb energy between energy groups

----------------------------------------------------------------

Is this something to worry about? Or just a problem of difference 
versions giving different levels of warnings?

Thanks in advance

-- 
Prof. Herbert de Castro Georg
Instituto de Física - Universidade Federal de Goiás
Campus Samambaia, CP 131, 74001-970, Goiânia, GO, Brasil
Tel: +55 62 3521-1014 Ramal 209
Fax: +55 62 3521-1014 Ramal 247