GROMACS version: 2019.4
Hi all,
I was simulating a membrane-protein system. The system worked well after temperature and pressure equillibration (see the 1st picture). Then I tried to introduce an oscillating electric field to it. At the beginning, when the field amplitude was 0.5 V/nm, the system looked fine. However, when the field amplitude was promoted to 1.0 V/nm, the system collapsed as seen in the 2nd picture. I have tried to remove the pressure equillibration, but the system still collapsed. I am thinking the electric filed must bring something wrong. But I don’t know what is wrong. What should I do to avoid this issue? Does anyone have clues on this? Many thanks.
Below I have attached the parameter file where the field was added. The forcefield is amber14sb.
define =
integrator = md
dt = 0.002 ; ps
nsteps = 50000000 ;100 ns
energygrps =
nstcomm = 100
comm_mode = linear
comm_grps = DMPC D2R_RIS Water_and_ions
refcoord-scaling = com
;
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 50000
nstenergy = 50000
nstxout-compressed = 5000
compressed-x-grps = system
;
pbc = xyz
cutoff-scheme = Verlet
coulombtype = PME
rcoulomb = 1.2
vdwtype = cut-off
rvdw = 1.2
DispCorr = EnerPres
;
Tcoupl = V-rescale
tau_t = 0.2 0.2 0.2
tc_grps = DMPC D2R_RIS Water_and_ions
ref_t = 303.15 303.15 303.15
;
gen_vel = no
gen_temp = 303.15
gen_seed = -1
; //// I have tried to use
;Pcoupl = parrinello-rahman
;pcoupltype = semiisotropic
;tau_p = 2.0
;ref_p = 1.0 1.0
;compressibility = 4.5e-5 4.5e-5
;
freezegrps =
freezedim =
constraints = hbonds
constraint_algorithm = LINCS
continuation = yes
electric_field_z = 1.0 25.1327 0 0
