[gmx-users] Parallel pulling with Gromacs 4.0.7: COMM mode problem

[chris.neale at utoronto.ca]

Correction: what you are actually doing is pulling your solute to the  
(X,Y) center of mass of your surface + (2.0 * 0.001/ps) nm in X + the  
initial center of mass distance in X and Y.

-- original message --

Dear Aykut,

Please give a more complete description of 1) the .mdp options and
expected behaviour that you get with gmx 3.3.3 on a single core and 2)
the .mdp options and difference that you get with gmx 4.0.7 in parallel.

For example, the following text is difficult to understand and doesn't
match with the .mdp options that you provide below: "the surface moves
in the opposite direction of motion and you have the pulling
coordinates in absolute coord"

That said, I'll take a guess that your problem is related to your X*Y
only (no Z) pull group:

pull_dim                 = Y Y N

That you seem to think will include some Z component:

pull_init1               = 2.0 0.0 1.0

But what you are actually doing is pulling your solute to the (X,Y)
center of mass of your surface + (2.0 * 0.001/ps) nm in X.

Which seems strange given that you are using semi-isotropic pressure
coupling ... a method intended to treat the Z dimension in a special
way, and not the X dimension.

Finally, you could easily test for yourself what happens when you run
gmx 4.0.7 in serial so that you could compare to gmx 3.3.3 in serial
and thus simplify the issue here.

Chris.