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

[Berk Hess]

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,
> 
> 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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