GROMACS SMD for TCR–pMHC: should TCR be pull group 1 or 2

User discussions
,
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question

I am setting up constant-velocity SMD for a TCR–pMHC system. The C-terminal Cα of the MHC α-chain is position-restrained as the anchor, and the pulling coordinate is defined by the vector connecting the CoM of the TCR and the MHC α-chain, aligned along the x-axis. A virtual harmonic spring is attached to the TCR CoM and moved along +x at constant velocity.

My question is:

In the GROMACS pull code, should the TCR be pull group 1 and the MHC be pull group 2 with pull_coord1_groups = 1 2, or is it better the other way around?

This is my current pull set up:

pull                    = yes       ; Center of mass pulling will be applied on 1 or more groups using 1 or more pull coordinates.
pull_ncoords            = 1         ;  we have only one reaction coordinate 
pull_ngroups            = 2         ; two groups defining one reaction coordinate 
pull_group1_name        = TCR 
pull_group2_name        = MHC_anchor 
pull_coord1_type        = umbrella  ; harmonic potential
pull_coord1_geometry    = direction ; Pulling along x-axis 
pull_coord1_dim         = Y N N     ; 
pull_coord1_vec         = 1 0 0
pull_coord1_groups      = 1 2
pull_coord1_start       = yes      ; define initial COM distance > 0
pull_coord1_rate        = 0.01     ; 0.01 nm/ps = 10 nm/ns
pull_coord1_k           = 100      ; kJ mol^-1 nm^-2
pull_print_components   = yes      ; 
pull_print_ref_value    = yes
pull_nstxout            = 500      ; value taken from paper
pull_nstfout            = 500

Also, When I used

pull_group1_name = TCR

pull_group2_name = MHC_anchor

pull_coord1_groups = 1 2

pull_coord1_vec = 1 0 0

pull_coord1_rate = +0.01

My smd_pullx.xvg, the coordinate starts negative (~ -4.95 nm) and only becomes positive after ~800 ps. For example:

t = 0 ps → -4.95 nm

t = 500 ps → -2.09 nm

t = 800 ps → ~0 nm

t > 800 ps → positive

Also, I explicitly verified the orientation beforehand using MDAnalysis, and the MHC → TCR vector is aligned along +x (TCR is physically to the right of MHC).

Does this mean that the pull coordinate behaves like:

r ≈ COM(MHC) − COM(TCR) which is opposite of what I expected from the group1/group2 definition), or is there is some other reason for it?