[gmx-users] pull code problem

[Andrei Neamtu]

Hi Berk,
thank you for the reply

here is my mdp file:

;

;	User aneamtu	

;	Joi, 7 mai - 2009

;	Input file

;

title                  =  Production_runs

;define                 =  -DPOSRES -DPOSRES_CA2+_IONS



;constraints           =  all-bonds



integrator             =  md

dt                     =  0.001	

nsteps                 =  50000	



nstcomm                =  1

nstxout                =  1000

nstvout                =  1000

nstfout                =  1000

nstlog                 =  500
nstxtcout              =  50
xtc_grps               =  Protein_ions


nstenergy              =  100

nstlist                =  10

ns_type                =  grid


coulombtype            =  PME

rlist                  =  1.0

rcoulomb               =  1.0

rvdw                   =  1.0
optimize_fft           =  yes


Tcoupl                 =  v-rescale

tc-grps		       =  Protein   SOL   ions

tau_t                  =  0.1       0.1   0.1

ref_t                  =  310       310   310



energygrps             =  Protein  SOL CA2+ NA+ CL-



Pcoupl                 =  berendsen

Pcoupltype             =  isotropic

tau_p                  =  0.5

compressibility        =  4.5e-5

ref_p                  =  1.0



gen_vel                =  no

gen_temp               =  310.0

gen_seed               =  173529



pull                   =  constraint
pull_geometry          =  distance
pull_dim               =  Y Y Y
pull_nstxout           =  10
pull_nstfout           =  10
pull_ngroups           =  2
pull_group0            =  Protein

pull_group1            =  CA2+1
pull_rate1             =  0.3

pull_group2            =  CA2+2
pull_rate2             =  0.3


I do not understand what I do wrong..
Should I use a -pi pull.ppa file like in gromacs 3.x ?

Andrei