[gmx-users] pull COM "geometry = direction periodic" problem

edesantis edesantis at roma2.infn.it
Thu Jul 20 10:18:43 CEST 2017

dear all,

I am studying the affinity between an antibody and an amyloid peptide;
I am interested in the evaluation of the PMF.

I tried to preform the COM pulling simulation using the "pull-geometry = 
direction", but for same the configurations (the ones in which the COMs 
of the two groups are quite far) I found the problem:
"Distance of pull group 1 is larger (...) than 0.49 times the box size ( 
... ). You might want to consider using "pull-geometry = 
direction-periodic" instead."

so according to the given suggestion, I tried to pull with the 
"pull-geometry = direction-periodic",
in this case I found the error :
"Fatal error:
184 particles communicated to PME rank 13 are more than 2/3 times the 
cut-off out of the domain decomposition cell of their charge group in 
dimension y.
This usually means that your system is not well equilibrated. "

the system is well equilibrated (according to the RMSD), the starting 
.gro file for gmx grompp is the same used for the geometry direction, 
and also the .mdp file is the same, except for the pull geometry 

so I don't understand what is the problem,

this is the COM part of the .mdp file used

; Pull code
pull                    = yes
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = Chain_Abeta
pull_group2_name        = Chains_Antibody
pull_coord1_type        = umbrella      ; harmonic biasing force
pull_coord1_geometry    = direction-periodic
pull_coord1_groups      = 1 2
pull_coord1_vec         =  38.207 68.611 29.8493
pull_coord1_rate        = 0.002        ;
pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
pull_coord1_start       = yes           ; define initial COM distance > 

any of you have suggestions?

thanks in advance for your help

Emiliano De Santis

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