Comm-mode setting in applied field simulation in membrane-protein complex

User discussions
1

GROMACS version:2021.5
GROMACS modification: No

Dear users,

I am running an applied field simulations and facing issue with setting the center of mass removal. As I am doing mutational study on the protein, the initial runs were done using a position restraint of 100 on the CA atoms, later on the same simulation were performed without restraints and there was issues as the whole system started drifting upwards in Z direction(axis of electric field)(to be noted here the comm-mode=linear). This also had impact of current calculation and water permeation calculation(which reduced significantly). So should I use the center of mass removal or not, or should I just use COM removal for X,Y axis and not Z(direction of electric field), or is it okay to use the restraints?

For your reference the mdp parameters I am using is :

include
;define = -DPOSRES

; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 25000000
; For exact run continuation or redoing part of a run
init-step = 0
; Part index is updated automatically on checkpointing (keeps files separate)
simulation-part = 1
; Multiple time-stepping
mts = no
; mode for center of mass motion removal
comm_mode = None
; number of steps for center of mass motion removal
nstcomm = 100
; group(s) for center of mass motion removal
comm_grps = SOLU_MEMB SOLV

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = v-rescale
nsttcouple = -1
nh-chain-length = 10
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc_grps = SOLU MEMB SOLV
; Time constant (ps) and reference temperature (K)
tau_t = 1.0 1.0 1.0
ref_t = 300 300 300
; pressure coupling
pcoupl = no
pcoupltype = semiisotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
; Scaling of reference coordinates, No, All or COM
refcoord-scaling = No

; Electric fields
; Format for electric-field-x, etc. is: four real variables:
; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps),
; and sigma (ps) width of the pulse. Omega = 0 means static field,
; sigma = 0 means no pulse, leaving the field to be a cosine function.
electric-field-x = 0 0 0 0
electric-field-y = 0 0 0 0
electric-field-z = -0.0931 0 0 0

I would be very thankful for your help regarding the same!!

2

You could use center of mass motion removal on the protein alone. But then I would think that the solvent will move the other way. If you protein has net charge, then the correct response is that it starts moving along the field. You could remove center of mass motion of both the protein and the solvent, but then you will suppress the, correct, physical response of the system.

3

Dear Hess,

Thank you for your reply! I would like to add further detail of my system for clarity, I am using a biological nanopore embedded in a lipid bilayer, and I want to study the water flow through the nanopore. Hence the system has a 1 M KCL concentration and a applied electric field of 1V. In this case If I use the center of mass removal(comm-mode=linear) the protein-membrane shows slow drift as the protein consists a net negative charge. If I use no center of mass removal (comm-mode=none) the system drifts very fast. So to overcome this I have applied a small restraint on particular C-alpha atoms of the protein which keeps the protein-membrane stable in the box. Though this solves the problem of drifting system in both the cases (comm-mode=none/linear), I currently wonder, how should I proceed, should I use COM removal for the system anymore. I hope this reference graph would be helpful and I would be thankful for insights!

The graph shows water permeation due to the application of -1V(determines the direction of water flow) in two conditions, red is with linear COM removal and black is with no COM removal, in both the condition the protein was restrained.

none_linear_vres
none_linear_vres792×612 4.37 KB

4

I would think that the best solution is to apply COM motion removal only on the protein. No restraints.