[gmx-users] CHARMM Pulling LINCS Error
Todd 53148
todd53148 at gmail.com
Thu Jun 18 19:40:19 CEST 2015
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
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