[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

Steve Fiedler fiedler at umich.edu
Thu Jan 22 19:22:24 CET 2009

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

More information about the gromacs.org_gmx-users mailing list