[gmx-users] Rigid nanotube

[Steven Neumann]

Dear Gmx Users,

I have 5 types of atoms which create a shape of the nonotube. 5 types of
beads correspond to future appliaction to which I will attach protein. I
wish the nanotube to be rigid and move in XY directions only. I created
bonds between all of them with app. b0=0.34 nm and a force constant of
10e5. I also used bonds within circles creating the tube with the same
force constant and the b0=7.46 nm (diameter of the tube) to make the tube
rigid. I exluded all non-bonded interactions nrexcl 8 as the cutoff = 2 nm
in my tabulated potentials. My mdp:

integrator               = md
tinit                    = 0.0
dt                       = 0.002
nsteps                   = 500000
nstcomm                  = 100
nstcalcenergy         = 100

nstxout             = 0
nstvout               = 0
nstenergy            = 0
nstlog                   = 100
nstxtcout                = 100

freezegrps         = System
freezedim          = N N Y
energygrps               = ACI BAS GLY NON POL
energygrp_table          = ACI ACI ACI BAS ACI GLY ACI NON ACI POL BAS BAS
BAS GLY GLY GLY GLY NON GLY POL NON BAS NON NON POL BAS POL NON POL POL
table-extension         = 1.0


nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 2.0


coulombtype          = User
rcoulomb                 = 2.0

vdw_type                 = User
rvdw                     = 2.0


tcoupl               = V-rescale
tc_grps               = System
tau_t                 = 0.1
ref_t                 = 300
pcoupl             = no

gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = -1


constraints              = all-bonds
constraint_algorithm     = Lincs
continuation             = no
lincs_iter              = 1
lincs_order              = 4



I get many LINCS warnings and errors and the simulation blows up. I
decreased the time step to 0.2 fs and then it works fine. However with this
performance my coarse-grain model does not make any sense. Would you
recommend distance restraints or sth else to have a better time step?

Please, advise,

Steven