[gmx-users] issues running virus capsid simulation

[Asis Jana]

Hi,

I am doing viral capsid simulation using GROMACS 2018. The capsid was first
energy minimized using the steepest-descent algorithm followed by 40 ns of
NVT (300 K) followed by 10 ns of NPT (300 K, 1 atm) equilibration. In the
NVT and NPT equilibration, the heavy atoms of the protein were restrained
with a force constant of 1000 kJ/mol/nm. Production MD simulations were
performed for 400 ns at a temperature of 300 K and a pressure of 1 atm.
Please see the production mdp file below.

title           = MD simulation
; Run parameters
integrator      = md
nsteps          = 2000000000
dt                  = 0.002
; Output control
nstxout                 = 50000
nstvout                 = 50000
nstenergy               = 50000
nstlog                  = 50000
nstxout-compressed  = 50000

compressed-x-grps   = System

continuation            = yes
constraint_algorithm    = lincs
constraints                 = h-bonds
lincs_iter                  = 1
lincs_order                 = 4
; Neighborsearching
cutoff-scheme   = Verlet
ns_type             = grid
nstlist                 = 20
rlist                   = 1.2
coulombtype             = pme
rcoulomb                = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 1.0
rvdw                    = 1.2
pme_order           = 4
fourierspacing  = 0.16
; Temperature coupling is on
tcoupl          = Nose-Hoover
tc-grps         = Protein Non-Protein
tau_t           = 1.0     1.0
ref_t           = 300     300
; Pressure coupling is on
pcoupl                  = Parrinello-Rahman
pcoupltype              = isotropic
tau_p                   = 5.0
ref_p                   = 1.0
compressibility     = 4.5e-5
refcoord_scaling    = com
; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC
; Dispersion correction
DispCorr        = EnerPres      ; account for cut-off vdW scheme
; Velocity generation
gen_vel         = no            ; Velocity generation is off
nstcomm                 = 100
comm_mode               = linear
comm_grps               = Protein Non-Protein

I have attached RMSD and Rg plots with this mail. It looks like that capsid
is stiil not equilibrated. Rg is increasing rapidly, whereas RMSD of the
capsid is increasing slowly. Please see the attached plots.  Any kind of
advice or suggestions are deeply appreciated.

Thanks in advance,
Asis