GROMACS version: GROMACS-2020.3-GPU
GROMACS modification: No
Hi everyone,
Recently I want to do a constant spped shear simulation using GROMACS. So I construct a water box to test, but I meet some questions. The basic idea refers to the shear simulation in the Reference guide (https://manual.gromacs.org/current/reference-manual/special/shearing.html), where it mentions the possibility of using the free energy lambda-coupling method to achieve constant velocity shearing. And I tried this method in a test water. The system is in NVT ensemble, and there are two walls at z =0 and z = box length.The bottom 1 nm water layer is freezed in x/y/z directions, the top 1 nm water is freezed only in z-direction. And the restrain .gro file used in grompp command -r, in which the x-coordinates of water molecules in the top water layer are plus 1 to represent the B-state. However, the shear didn’t happend and I’m cofused. The mdp parameters is as below:
; Run Control
integrator = md ; leap-frog integrator of Newton’s equations of motion
tinit = 0 ; [ps] starting time for the run
dt = 0.001 ; 2 fs - [ps] time step for integration
nsteps = 100000 ; 1000 ps
; Output Control
nstxout = 1000 ; save coordinates every 10 ps
nstvout = 1000
nstenergy = 1000 ; save energies every 1 ps
nstlog = 1000 ; update log file every 100 ps
; Bond parameters
constraints = h-bonds ; convert all bonds to constraints
constraint-algorithm = lincs ; holonomic constraints
; Neighbor searching and nonbonded interactions
cutoff-scheme = verlet ; Cutoff-related parameters
nstlist = 10 ; Frequency to update the neighbor list and the long-range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
pbc = xy ; Use periodic boundary conditions in all directions
rlist = 0.9 ; [nm] Cut-off for making neighbor list (short range forces)
comm-mode = None
; Electrostatics
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 0.9 ; [nm] Short-range electrostatic cut-off
ewald-geometry=3dc
; Van der waals
vdwtype = cutoff
rvdw = 0.9 ; [nm] Short-range Van der Waals cut-off
; Temperature coupling
tcoupl = v-rescale ; Temperature coupling, modified Berendsen thermostat
tc_grps = System ; Group to couple to separate temperature baths
tau_t = 0.1 ; [ps] Time constant for coupling
ref_t = 300 ; [K] Reference temperature for coupling
;non-equ
;acc_grps = top_water
;accelerate = 0 0 0
freezegrps = top_water bottom_water
freezedim = N N Y Y Y Y
;deform = 0 0 0 0 0.1 0
nwall =2
wall_type = 12-6
wall_atomtype = O O
wall_r_linpot = 1
free-energy = yes
init-lambda = 0
delta-lambda = 0.1
Maybe I don’t understand the key of this method or miss something important. I was hoping that someone can help me. Thank you so much! And if there’s any other method to inplement the constant speed shear simulation in GROMACS, please share with me. Thanks again!
Regards,
Feng xuan