How can I pull 1 out of several molecules towards bilayer center

User discussions
1

GROMACS version: 2020.2
GROMACS modification: No
I have 302 molecules in my bilayer systems. The molecules are mostly located at the interface of the bilayer. I want to pull just one of the molecule to the center of the bilayer. I have applied position restraint to the bilayer. But How can I apply position restraint to this 301 molecule and just pull 1 of them.

2

You should not use position restraints. You should use the pull code with geometry=cylinder and have the membrane as reference group and one molecule as the other pull group. There are many publications with the setup and probably also tutorials.

3

Thanks for the suggestion. The pull group i intend to pull is just one among many. What If all of them get pulled if I do not apply constraint. That’s my confusion.

4

That depends a bit on what you want to combine. You can pull many groups with respect to the same bilayer reference group.

5

; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = PDMS
pull_group2_name = DMPC
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = cylinder ; simple distance increase
pull_coord1_dim = N N Y
pull_coord1_vec = 0 0 1
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = -0.005 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 3000 ; kJ mol^-1 nm^-2
pull_nstxout = 1
pull_nstfout = 1
; ENFORCED ROTATION
rotation = yes
rot_ngroups = 1
rot_group0 = DMPC_DMS
rot_type0 = rm2-pf
rot_vec0 = 0.0 0.0 1.0
rot_pivot0 = 0.0 0.0 0.0
rot-massw0 = no
rot_rate0 = 0
rot_k0 = 4000
rot_eps0 = 0.01
Is the above defination of mdp file correct?

6

group 1 should be the bilayer, which I guess it is not in your file.

Why do use the enforced rotation code?

7

Do you mean that the selection groups that you use for pulling contain multiple molecules instead of just one? I.e., are there multiple PDMS molecules in the PDMS selection group? If that is the case then you just have to add a new selection group, containing just the molecule you want to pull, to your index file. And then you use that as pull group instead.

8

I have 302 DMS. Among them I want to pull a single DMS to bilayer center, which I have renamed as PDMS and created an index of it. Similarly in the itp I have copied DMS itp and renamed DMS to PDMS to create a new itp. This new itp i inserted in the top making sure [moleculetype] defination in the gro file and top file are matching. Now I am pulling using the mdp and I have now removed rotation restraint. Still I get error.

9

It’s still not clear exactly what error you are getting, which means that it’s difficult to help you. Have you followed Berk’s instructions and set pull_group1_name = DMPC and pull_group2_name = PDMS?

10

hi. i have a similar question!. i am a beginner PhD student in the field of md simulation and want to use umbrella sampling to study the permeation of my nanoparticle through a membrane. my system contains “ions, water, nanoparticle and membrane”
i prepared 2 groups in my index file: (1) nano | (2) other (contain membrane, water and ion). is it correct as i just want to pull my nanoparticle?

so is this pulling code in my mdp file ok or i should modify it?

; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = other
pull_group2_name = nano
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = direction ; simple distance increase
pull_coord1_vec = 0 0 1
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

thank you for your consideration.

11

I would suggest making a new index group with only the membrane. Then set pull_group1_name = membrane (if that is what you called the index group). There’s no reason to involve the water and ions in the pulling.

13

thank you so much for your kind answer.

but I have a few questions that I would be very grateful if you could help me as I don’t have an informed person around me to help me and my readings have confused me.

1- If I don’t include “water and ions”, what will happen to them during pulling?
2- In similar codes for “pull-coord1-geometry” I have seen “distance, direction and cylinder” geometries. What is their difference? How do I know which geometry is better?
3- I have seen that “pull-group1-pbcatom” and “pull-group2-pbcatom” are used in some codes. What is the reason and how is the number (COM) attributed to them determined?
4- Is “pull_group1_name” always the fixed group and “pull_group2_name” the group on which the pull is to be performed?
5- how large the pull group should be to use “pull-pbc-ref-prev-step-com”?
6- Finally, a very trivial question, how do I know that the “pull_coord1_rate” and “pull_coord1_k” used were appropriate for my system?!

14
  1. The water and ions will be unaffected by the pulling.
  2. There is some more information at https://manual.gromacs.org/current/user-guide/mdp-options.html#com-pulling. For pulling through a membrane cylinder is usually a good choice, especially if the membrane is flexible, but direction usually works fine as well. More information is also available in https://manual.gromacs.org/current/reference-manual/special/pulling.html.
  3. This is also described in the links above. Large selection groups need a periodic boundary treatment, and one atom is used as a reference to find the closest (to the reference atom) periodic image of all atoms in the group. The atom number is based on the atom number in the coordinate system (not only the selection group). You will never go wrong if you pick a centrally located atom.
  4. The first of the pull-coord?-groups is the reference group.
  5. That is also described in https://manual.gromacs.org/current/reference-manual/special/pulling.html. There is no specific rule, but if you have a very large group (let’s say group1) and your pull-group1-pbcatom moves so much (relative to the rest of the group) that other atoms end up in another periodic image you will see large fluctuations in the position of your pull group. Using the center of mass (of the previous step) as reference will avoid that. If you choose a centrally located atom you can (almost?) never go wrong if you choose pull-pbc-ref-prev-step-com.
  6. It is difficult to know exactly what rate and force constant you should use. It will depend on what you want to study. There is no general answer. Have a look at the trajectories to see that nothing seems to break or distort too much. Run your analyses and check that they make sense. If your force is not high enough it might be difficult to pass through very resistive regions - your pulled group will not be close to the pulling target coordinate.

I hope that helps.

15

dear MagnusL
thank you so much for your time and consideration.