Umbrella sampling and cylinder geometry

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GROMACS version: 2021.3
GROMACS modification: No
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I am looking forward to perform umbrella sampling for permeation of a solute through a bilayer membrane.
I have added the following to my mdp.

pull = yes
pull-coord1-type = umbrella
pull-coord1-geometry = cylinder
pull-cylinder-r = 2.0
pull_nstxout = 100
pull_nstfout = 100
pull-coord1-dim = N N Y
pull_constr_tol = 1e-06
pull_ngroups = 2
pull-group1-name = MEM
pull-group2-name = SOL
pull-coord1-groups = 1 2
pull-coord1-start = no
pull-coord1-init = 0.1
pull-coord1-rate = 0
pull-coord1-k = 1000
pull-coord1-kB = 1000

When going through literature, I found that several groups have used lipids within a cylinder with internal diameter 1.5 nm and external diameter 2 nm as reference for COM. The weight at 1.5 nm was 1 and decreased linearly to 0 at 2 nm. The cylinder was centered at the solute and aligned with z-axis.

I have the following questions:

  1. Using pull-cylinder-r = 2.0, the weight of atoms change from 1 at the centre of the cylinder to 0 at the 2 nm. How do I change this such that the weight at 1.5 nm from centre of cylinder is 1 and decreases to 0 at 2 nm?
  2. US is generally reported with window spacing of 0.1 nm or lower. However, given the system size that I am working, even a 0.1 nm window is going to be really costly. Is there a computationally faster way (>0.1 nm window size, alternates to US like TI, etc.) that I may explore to compare permeation of different solutes? I am using MARTINI FF and the system size easily reaches 250K+ Martini beads.
  3. For US, are there any additional options (apart from those listed above) that should be added to the mdp?

Thanks!
Raman

2

Adding to my previous post, there were options pull-r1 and pull-r0 in Gromacs 4.x but these do not appear in manuals of 20xx versions. Are these options still supported in any recent Gromacs versions? If not, are there any workarounds to implement these?

Thanks!
RPS

3

The old setup with two radii was mathematically and physically incorrect. The new setup with the same outer radius is not that much different from the old one.

The required umbrella window spacing depends completely on your setup. I would think that you should be able to use a larger spacing when using a coarse-grained system.

4

Dear Hess,

Thank you for the background and the inputs.

Regards,
RPS