[gmx-users] pull code problem

[Jian Dai]

Hi, all:
I tried to pull a specific DPPC, say, r3, out of a pre-equilibrated bilayer
into the water along the positive z axis. For the pull code parameters, I
used:
pull                       = umbrella
pull_geometry        = distance
pull_vec1               = 0. 0. 1.
pull_dim                = N N Y
pull_nstxout          = 1000
pull_group0           = bilayer
pull_group1           = r3_P
pull_k1                 = 500
pull_rate1             = 0.001        ;nm/ps
integrator              = md
dt                         = 0.002 ;ps
nsteps                  = 1000000
nstcomm              = 1
comm_grps           = DPP SOL
nstxtcout               = 100
nstlist                 = 10
ns_type                 = grid
pbc                     = xyz
rlist                   = 1.0
coulombtype             = PME
rcoulomb                = 1.0
vdwtype                 = cut-off
rvdw                    = 1.0
ewald_rtol              = 1e-5
optimize_fft            = yes
tcoupl                  = Berendsen
tau_t                   = 0.1        0.1
tc_grps                 = DPP        SOL
ref_t                   = 323        323
pcoupl                  = Berendsen
pcoupltype              = semiisotropic
tau_p                   = 1.0         1.0
compressibility         = 4.5e-5     4.5e-5
ref_p                   = 1.0         1.0
gen_vel                 = no
gen_temp                = 323
gen_seed                = 173529
constraints             = all-bonds
constraint_algorithm    = LINCS
lincs_order             = 4

"r3_P" corresponds to an index file that contains the phophorus group of r3,
and "bilayer" corresponds to an index file that contains all the lipids
except r3.

I'm using GROMACS 4.0.3, but when I looked at the trajectory in VMD, the
position of r3 is hardly moved. So what's the right way to pull this
specific lipid into the water slab?

Thanks.

dj
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