Pull the whole system with pull code

User discussions
1

GROMACS version:2021.2
GROMACS modification: No
Dear all,
I would like to pull the NaCl solution with a fix rate, e.g. 0.0001nm/ps, to give the whole system a fix flow rate,
is it possible to do it with pull code in GROMACS?
I have made a test and calculated MSD of ions in three dimensions,
it seems that there is no obvious difference in the three directions (I pull the system along z direction).
Here is my pull setting:
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 1 ; two groups defining one reaction coordinate
pull_group1_name = system
;pull_group2_name = Protein
pull_coord1_type = umbrella
pull_coord1_geometry = direction-periodic
pull-group1-pbcatom = -1
pull-pbc-ref-prev-step-com = yes
pull_coord1_dim = N N Y
pull-coord1-vec = 0 0 1
pull_coord1_groups = 0 1
;pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.0001 ; restrain in place
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2

Thanks in advance.
Regards,
Bin Li

2

Hi,
Just a suggestion. You try to use acc_grp and accelerate Molecular dynamics parameters (.mdp options) — GROMACS 2021.3 documentation. The options are deprecated, since they are not working in some specific condition, but maybe in your case it works.

Best regards
Alessandra