How to pull a molecule across the bilayer?

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GROMACS version: 2019.4
GROMACS modification: No
integrator = md
dt = 0.002
nsteps = 5000000
nstxout = 500
nstvout = 500
nstfout = 500
nstcalcenergy = 100
nstenergy = 100
nstlog = 100
;
cutoff-scheme = Verlet
nstlist = 20
rlist = 1.2
coulombtype = pme
rcoulomb = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
;
tcoupl = Nose-Hoover
tc_grps = SYSTEM
tau_t = 1.0
ref_t = 303.15
;
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 = SYSTEM
;
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 = lipids
pull_group2_name = POL
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_dim = N N Y ; pull along z
pull_coord1_groups = 1 2 ;
pull_coord1_start = yes ; define initial COM distance > 0
pull-pbc-ref-prev-step-com = yes
pull-coord1-geometry = cylinder
pull_coord1_vec = 0.0 0.0 1.0
pull_coord1_rate = 0.0001 ;
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2

I have already posted this on the forum and still couldn’t resolve the issue. So I am posting it again. The above is my pull code. I am trying to pull a small molecule POL across the bilayer. The molecule seems unaffected by the pull command. The molecule fluctuate in the middle of the bilayer. I have tried various values for k and rate, still no update with result. Could anyone guide me thru this?

1 Like
2

Hi @drrahulsuresh,
Please see the paper here.

I would like to know is POL hydrophilic or hydrophobic? You can change the rate to 0.01 or -0.01 and see if there is any difference. As a beginner I am also struggling to pull a carbohydrate molecule across bilayer. So it would be great to see you solve this issue.
Thanks and regards.
Anirban

3

Hi
The molecule is 1,3 butadiene. its hydrophobic. I have already tried with different values of rate. I will try this as well.
Thank you @Anirban12

4

If I reduce the rate to 0.01 or -0.01 i end up with error “Distance between pull groups 1 and 2 (4.130297 nm) is larger than 0.49 times the box size (4.130255)”

5

Hi @drrahulsuresh
The negative rate actually does opposite of what positive rate does [push towards membrane or pull from membrane]. And this particular error is because POL now can see periodic image of the membrane, the distance between groups cannot be more than box/2.
Does the position of POL changes now? If it does not, u can try with higher k value like 1500 or 2000. You can also change the geometry from cylinder to distance and check. Hope these will help you.
Thanks and Regards
Anirban

6

Hi. Sorry for very late reply. Gor occupied with other bunch of works. Actually it didn’t work. Still at the same place