[gmx-users] NVT simulations for poylsaccharides in CHARMM36

[Jivesh Madan]

I was doing NVT simulations on a structure constituting of 3 monomers of
AGLC residue(glucose molecule) connected via 1-4 linkage.
Though I have modified my nvt.mdp file for CHARMM36 but still encountering
errors.
The following is the nvt.mdp and I am also attaching the topology file
topol.top with it.


define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; removing CM translation and rotation
;comm_mode       =  ANGULAR
;nstcomm         =  1
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
dwtype         = cutoff
ns_type         = grid          ; search neighboring grid cells
nstlist         = 5             ; 10 fs
rlist           = 1.2
rlistlong       = 1.2
rvdw-switch     = 1.0           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = Berendsen ; modified Berendsen thermostat
tc-grps = System Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 330 330 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 330 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
cutoff-scheme = Verlet



These are the errors which I am facing

NOTE 1 [file nvt.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 2905043056
Generated 85052 of the 85078 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 55198 of the 85078 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Other'
turning H bonds into constraints...
Setting gen_seed to 475227507
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet

WARNING 1 [file topol.top, line 699]:
  The bond in molecule-type Other between atoms 3 O1 and 4 A1 has an
  estimated oscillational period of 9.1e-03 ps, which is less than 5 times
  the time step of 2.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Analysing residue names:
There are:     3      Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...

-------------------------------------------------------
Program gmx, VERSION 5.0.2
Source code file:
/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/readir.c,
line: 3205

Fatal error:
Invalid T coupling input: 3 groups, 1 ref-t values and 1 tau-t values