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

[Chris Neale]

I just checked similar simulations of mine and Berk's suggestion 
accounts for similar discrepancies that I notice on a quick evaluation 
where g_traj and g_dist fail to give me the same distance as I obtain 
from the pull pos.xvg file. As Berk suggests, once I first trjconv 
-center -pbc mol -ur compact (giving an appropriate residue for 
centering that puts all relevant pulled atoms in the same box) then 
g_traj and g_dist both give me the exact same answer as I calculate 
based on pull pos.xvg. Chris -- original message -- Hi, There could be a 
problem with periodic boundary conditions. Do you have multiple 
molecules in a pull group, or broken molecules? In that case the COM 
position of 3.3.3 and g_traj are both incorrect. The pull code in 4.0 
grompp and mdrun are (as far as I know) always correct. Berk

> > Date: Thu, 22 Jan 2009 13:22:24 -0500
> > From: fiedler at umich.edu
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3	regarding pull_geometry=distance
> > 
> > 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,