[gmx-users] CHARMM Pulling LINCS Error

[Todd 53148]

Dear Gromacs Users,

I have been trying to pull my protein's center of mass away from the
alpha-carbon of a residue.  My pull group consists of non-hydrogens at
least 3 residues distant from the tether residue, which is restrained.

I am using implicit solvent in gromacs 4.5.5, pulling at 0.000005nm/ps with
a 0.002 dt.  I have equilibrated for 100ns, and I do not think that more
equilibration is necessary.  Equilibration generated no LINCS errors.

With pulling and restraint force constants of 3000kJ/(mol*nm^2), I
generated LINCS errors at about step 30 of the pull.  They were also
generated at a pulling rate of 0.  I was able to do the same experiment in
OPLS-AA with no LINCS errors.

I decreased the force constants to 1000, and only got a LINCS error for one
of 50 pulls (50 different residues' CAs).

Any advice on where I could be going wrong would be greatly appreciated.
An example mdp is below.

Thanks very much,

Todd

define          = -DPOSRES
integrator      = sd
nsteps          = 60000000
dt              = 0.002
comm-mode       = angular
nstxout         = 5000
nstvout         = 5000
nstfout         = 5000
nstenergy       = 5000
nstlog          = 5000
continuation    = yes
constraint_algorithm = lincs
constraints     = h-bonds
lincs_iter      = 1
lincs_order     = 4
ns_type         = simple
nstlist         = 0
rlist           = 0
rcoulomb        = 0
rvdw            = 0
coulombtype     = cut-off
tc-grps         = system
tau_t           = 2
ref_t           = 300
ld_seed         = -1
pcoupl          = no
pbc             = no
gen_vel         = no
implicit_solvent     =   GBSA
gb_epsilon_solvent   =   80
gb_algorithm         =   Still
rgbradii             = 0
pull            = umbrella
pull_geometry   = distance
pull_dim        = Y Y Y
pull_start      = yes
pull_ngroups    = 1
pull_group0     = Freeze
pull_group1     = Pull
pull_rate1      = 0.000005
pull_k1         = 1000
pull_nstxout    = 50
pull_nstfout    = 50