[gmx-users] pull code problem

[Berk Hess]

Hi,

First, please switch to 4.0.5, I have put several fixes in the pull code
in the 4.0 minor releases.

You did not specify pull_init1, nor pull_start, this means you start pulling 
at a distance of 0, which means the center of the bilayer.
Setting
pull_start = yes
should fix your problem.

Berk

Date: Thu, 6 Aug 2009 10:49:26 +0800
From: djpittdj at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] pull code problem

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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