GROMACS version:
GROMACS modification: Yes/No
Here post your question
I conducted a pulling simulation to analyze the interaction between a polymer and a membrane. The simulation continued in the membrane direction from the following configuration.
The polymer is represented in red.
The pulling.mdp file used is as follows:
plaintext
코드 복사
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 250000 ; 2 * 500000 = 1000 ps (1 ns)
dt = 0.002 ; 2 fs
; Output control
nstxout = 0 ; save coordinates every 2 ps
nstvout = 0 ; save velocities every 2 ps
nstxtcout = 500 ; xtc compressed trajectory output every 2 ps
nstenergy = 30000 ; save energies every 2 ps
nstlog = 30000 ; update log file every 2 ps
; Bond parameters
continuation = yes ; Restarting after NPT
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
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.2 ; 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 = v-rescale ; More accurate thermostat
tc-grps = SOL_ION LNPG MEMB ; three coupling groups - more accurate
tau_t = 0.5 0.5 0.5 ; time constant, in ps
ref_t = 253 253 253 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = berendsen ; Pressure coupling on in NPT
pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z
tau_p = 4.0 ; time constant, in ps
ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar)
compressibility = 3.0e-5 3.0e-5 ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no
;gen_temp = 253 ; Velocity generation is off
; COM motion removal
; These options remove motion of the protein/bilayer relative to the solvent/ions
nstcomm = 1
comm-mode = Linear
comm-grps = SOL_ION LNPG MEMB
refcoord_scaling = com
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = LNPG
pull_group2_name = LIPID
pull_group2_pbcatom = 14842
pull_pbc_ref_prev_step_com = yes
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = -0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
However, the following error occurred during the simulation:
“Pull reference distance for coordinate 1 (-0.000018) needs to be non-negative”
Could you please suggest how to resolve this issue?