GROMACS version:2019.6
GROMACS modification: No
When performing SMD simulations to study ligand dissociation from a protein, I encounter a challenge due to the large size of my protein. It seems impractical to create a 400 Å box to encompass the entire protein as the reference group for SMD.
However, if I choose only a part of the protein as the reference group, this section of the protein moves in the opposite direction to the ligand during the SMD process, which is undesirable. In such cases, how do others usually address this issue? Thank you very much.
My .mdp file is based on the one automatically generated by CHARMM-GUI after constructing the membrane system.integrator = md
dt = 0.002
nsteps = 1000000
nstxout = 5000
nstvout = 5000
nstfout = 500
nstcalcenergy = 100
nstenergy = 500
nstlog = 500
;
cutoff-scheme = Verlet
nstlist = 20
rlist = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
coulombtype = PME
rcoulomb = 1.2
;
tcoupl = Nose-Hoover
tc_grps = SOLU MEMB SOLV
tau_t = 1.0 1.0 1.0
ref_t = 310 310 310
;
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
;
nstcomm = 100
comm_mode = linear
comm_grps = SOLU_MEMB SOLV
;smd set
pull = yes
pull-ngroups = 2
pull-group1-name = N
pull-group2-name = R162
pull-ncoords = 1
pull-coord1-type = umbrella
pull-coord1-geometry = direction
pull-coord1-groups = 1 2
pull-coord1-rate = 0.003
pull-coord1-dim = Y Y N
pull_coord1-k = 100
pull-coord1-vec = -18.4 17.0 0.0
pull_coord1_start = yes
Best regards.