BOX Error in SMD simulation

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1

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Hello everyone,

I want to pull a ligand into the cyclopeptide nanotube (in z direction). i used position restrain to fix the movement of cyclopeptide .However, in the SMD simulation, I encountered the following error:

“Distance between pull groups 1 and 2 (7.796643 nm) is larger than 0.49 times the box size (7.796385 nm).”

Even though I manually set the box size to be larger than half the distance, I still encounter the same error.

I am a beginner and not sure if something is wrong with my md.mdp file. Could anyone help me troubleshoot this issue?

This is my md.mdp:

title = Pulling ligand through CP simulation
; Position restraints on CP backbone
define = -DPOSRES
; Run parameters
integrator = md
dt = 0.002
nsteps = 500000 ; 1000 ps
comm-mode = Linear
; Output control
nstxout = 5000 ; save coordinates every 10.0 ps
nstvout = 5000 ; save velocities every 10.0 ps
nstfout = 0 ; nstvout, and nstfout
nstenergy = 5000 ; save energies every 10.0 ps
nstlog = 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps
compressed-x-grps = System ; save the whole system
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = H-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.1 ; short-range electrostatic cutoff (in nm)
rvdw = 1.1 ; 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 ; modified Berendsen thermostat
tc-grps = Protein_LIG Water ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = C-rescale ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, 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 ; Velocity generation is off

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 = Protein ; name in index
pull_group2_name = lig ; name in index
pull-coord1-type = constant-force
pull_coord1_geometry = cylinder ; simple distance increase (I also used direction but got the same error)
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.001 ; 0.01 nm per ps = 10 nm per ns
pull-coord1-vec = 0 0 -1 ; Pulls along negative z-axis (into the nanotube)
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2

2

It’s unlikely that the error message is wrong. Is your box really taller than 15.6 nm?

And how can you pull the peptide when you fix it using position restraints?

3

Thank you, dear Hess.

At first, I used a smaller box and thought the issue was with the box size. Since I want to pull the ligand in the Z direction, I increased the box size in that direction.

Honestly, this is my first time attempting to pull a ligand into a nanotube. So, if I don’t pull the nanotube, how can I determine the reaction coordinate? Do you mean I should only pull the ligand?

Yes, I want the nanotube to remain fixed.

4

No, you wrote that you use position restrains on the peptide. That’s not consistent with you know saying that you want the nanotube to be fixed.

Do you also have solvent or only the nanotube and the peptide in the system?

The geometry should be direction, not cylinder.

5

Yes, I have water as the solvent.

I’m sorry, I’m a bit confused. Do you mean that I shouldn’t use position restraints on the peptide nanotube? If so, how can I fix its movement while pulling the ligand into it?

6

Ah, my mistake. I thought you are pulling a peptide through a tube, but it’s a ligand through a tube made of peptides.

I still think you would not need to restrain the tube. But you can. Restraining the tube affects its internal degrees of freedom also. I don’t see the issue with the COM of the tube moving a bit.

7

Thank you

So, do you think the issue resulted from the position restraints? I’ll give it a try.

Anyway, could you please check my pull sections? I’d be very grateful if you could inform me of any issues

Only change i should make is to use direction instead of cylinder, yes?

8

I have no idea what causes your issue. You pull section look ok, apart from the geometry.