Dear all,
In order to obtain the PMF diagram of a water molecule through membrane
protein channel, I set up a simulation system and try to run with
pull_coord1_geometry = direction-periodic. To correct te error following
changes are made in the mdp file {error (Can not have dynamic box while
using pull geometry 'direction-periodic' (dim
z))}
Pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 2.0
But now it shows
Pressure coupling incorrect number of values (I need exactly 2), can
anyone tell me what changes I need to make
my pulling parameters
pull = yes
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = Chain_B
pull_group2_name = Chain_A
pull_coord1_type = umbrella ; harmonic biasing force
pull_coord1_geometry = direction-periodic
pull-coord1-vec = 0 0 1
;pull-vec = 0 0 1 ; simple distance increase
pull_coord1_groups = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
pull_coord1_start = yes ; define initial COM distance > 0
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