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

[chris.neale at utoronto.ca]

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.

-- original message --

Hi everyone

I have a pulling code running in parallel (32 processors) with Gromacs 4.0.7
The systems composes of a surface and a protein

with Gromacs 3.3.3 (on single processors ) when I set the COMM mode for
the surface, the surface stands still,
and of course for the pulling code (reference groups is also surface) ,
the position of the protein is given /wrt the surface.
However for G4, no matter which group you set for COMM mode, the surface
moves in the opposite direction of motion and you have the pulling
coordinates in absolute coord. which is not what I want.

I want a pilling output /wrt the surface as in G3

Has anyone experienced smtg like this?
suggestions will be appreciated

Thanks
Aykut


*.mdp file
DIAM=surface
//////////////////////////////////////////

integrator               = md
nsteps                    = 30000000
dt                           = 0.002
nstlist                     = 50
nstxout                  = 20000
nstvout                  = 20000
nstfout                   = 20000
nstxtcout               = 4000
nstlog                    = 20000
nstenergy              = 20000
constraints             = hbonds
ns_type                 = grid
coulombtype         = pme
pme_order             = 4
fourierspacing           = 0.12
rlist                        = 0.8
rvdw                     = 0.8
rcoulomb               = 0.8
energygrps            = DIAM Protein SOL
tcoupl                   = berendsen
tc_grps                  = DIAM Protein SOL
tau_t                    = 0.1 0.1 0.1
ref_t                    = 300 300 300
gen_vel                  = yes
Pcoupl                   = berendsen
Pcoupltype               = semiisotropic
compressibility          = 2.5E-8 4.5E-5
tau_p                    = 1.0 1.0
ref_p                    = 1.0 1.0
comm_mode                = angular
nstcomm                  = 1
comm_grps                = DIAM

;PULLING
pull                     = umbrella
pull_start               = yes
pull_geometry            = position
pull_dim                 = Y Y N
pull_nstxout             = 200
pull_nstfout             = 200
pull_ngroups             = 1
pull_group0              = DIAM
pull_group1              = AA1
pull_vec1                = 1.0 0.0 0.0
pull_init1               = 2.0 0.0 1.0
pull_rate1               = 0.001
pull_k1                  = 50
///////////////////////////////////////////