Dear all,
I have encountered an odd behavior with use of the "pull_geometry =
distance" option of the pull code, upon transitioning from Gromacs
version 3.3.3 to version 4.0.3. It appears to be related to the center
of mass distances of the two pull groups, which has an effect of
abruptly displacing the coordinates of the less massive group. A
diagnostic is a discrepancy between the distances between the pull
groups from the preprocessor output in version 4.0.3, and the distance
between the groups as calculated using the difference of the groups'
centers of mass from the g_traj utility. For example, using the
coordinates of a system previously equilibrated with the constraint
force approach from version 3.3.3, the grompp output from version 4.0.3 is:
Pull group natoms pbc atom distance at start reference at t=0
0 2672 1336
1 60 6818 2.673 0.400
Using g_traj (4.0.3 version), the difference of the distance between the
center of masses of the two groups is: 0.39911 nm versus the 2.673 value
from above.
This issue does not exist in previous versions of Gromacs including
version 3.3.3. In version 4.0.3, this behavior occurs for both
pull=umbrella and pull = constraint, on 32 and 64 bit architecture
systems, and in both single and double precision calculations. A test
of a two atom system determined that the pull_start option was not
appropriate. The pull options used in the mdp file are listed below, as
well as the contents of the ppa file which has worked previously.
Suggestions would be appreciated,
Thank you,
Steve Fiedler
Gromacs 4.0.0 mdp pull options
pull = constraint
pull_geometry = distance
pull_dim = N N Y
pull_start = no
pull_init1 = .4
pull_group0 = Ref
pull_group1 = Buk
Gromacs 3.3.3 ppa file:
runtype = constraint
group_1 = BUK
reference_group = Ref
reftype = com
constraint_direction = 0 0 1
constraint_distance1 = 0.400
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