Hi everyone,
I have a pulling code running on single machine with Gromacs 4.0.7
The systems composes of a surface, a protein and water
I pull the protein from the terminal group on the surface laterally.
With Gromacs 3.3.3 (on single processors ) the setup works perfectly and
generates correct results for pulling positions compared to g_traj...
To be able use periodic molecules (for the surface), I switched to
gromacs 4.0.7 and I use the "position" option to reproduce the previous
v3 results.
The problem is that the pullf.xvg gives negative forces...
Normally, the pulling force should reach a pseudo-constant level but in
my case it just keep going toward minus infinity (unless I cease the run)
Also when I checked position of the pulled group I see that the tangent
of the displacement-time curve (which is th pulling rate) is also
increasing afte.
This is bit irrational since the pulling rate is set constant at the
first place...
For instance, with a pulling rate of 10nm/ns in 1ns you should have
displacement of roughly 10nm.
Untill 0.4 ns everything looks ok but then (when the peptide moves to
the next periodic box) velocity increases and I have a displacement of
more 150nm within 1ns...
Also, I must say that in the trajectory the increasing velocity of the
pulled can be seen clearly with naked-eye.
Here is my mdp file;
integrator = md
nsteps = 1000000
dt = 0.002
nstlist = 40
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstxtcout = 2000
nstlog = 5000
nstenergy = 5000
constraints = hbonds
ns_type = grid
coulombtype = pme
pme_order = 4
fourierspacing = 0.12
rlist = 0.8
rvdw = 0.8
rcoulomb = 0.8
energygrps = DIAM Protein SO
tcoupl = berendsen
tc_grps = DIAM Protein SOL
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
gen_vel = no
Pcoupl = berendsen
Pcoupltype = semiisotropic
compressibility = 2.5E-8 4.5E-5
tau_p = 1.0 1.0
ref_p = 1.0 1.0
comm_mode = angular
comm_grps = DIAM
periodic_molecules = yes
pbc = xyz
;PULLING
pull = umbrella
pull_start = yes
pull_geometry = position
pull_nstxout = 100
pull_nstfout = 100
pull_ngroups = 1
pull_group0 = DIAM
pull_group1 = AA1
pull_vec1 = 1.0 0.0 0.0
pull_init1 = 0.0 0.0 0.0
pull_rate1 = 0.01
pull_k1 = 100
Has anyone experienced smtg like this?
suggestions will be appreciated
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