GROMACS version: 2023.3
GROMACS modification: No
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I am trying to calculate the friction force in a system where a molecule is subjected to a harmonic spring in the X and Y dimensions and is pulled along the X-axis on a rough polymer slab (see attached figure). The polymer slab is frozen during this process, and the system was equilibrated before performing the pulling simulation. I expected the force data from pullf.xvg to represent the friction force. However, the force appears to increase linearly over time. I am unsure if there is an issue with my input parameters (provided below). Has anyone encountered a similar problem or have any suggestions for resolving this?
Thank you.
integrator = md
dt = 0.001
nsteps = 2000000
nstxout = 1000
nstvout = 1000
nstenergy = 1000
nstlog = 1000
nstxout-compressed = 10000
compressed-x-grps = System
cutoff-scheme = Verlet
nstlist = 10
rcoulomb = 1.4
rvdw = 1.4
pbc = xyz
DispCorr = no
coulombtype = PME
pme_order = 4
fourierspacing = 0.12
tcoupl =Nose-Hoover
tc-grps = system
tau_t = 0.2
ref_t = 298
pcoupl = no
continuation = no
constraint_algorithm = lincs
constraints = none
lincs_iter = 1
lincs_order = 4
lincs_warnangle = 30
morse = no
gen_vel = no
gen-temp = 298
gen-seed = -1
;*************
; Pull code *
;*************
pull = yes
pull-ncoords = 1
pull-ngroups = 1
pull-nstxout = 1000
pull-nstfout = 1000
pull-xout_average = no
pull-fout_average = no
pull-group1-name = PTM
pull-coord1_type = umbrella
pull-coord1_geometry = direction
pull-print-components=yes
pull-coord1_dim = Y Y N
pull-coord1_groups = 0 1
pull-coord1-origin = 0.0 0.0 0.0
pull-coord1_vec = 1.0 0.0 0.0
pull-coord1_start = yes
pull-coord1_rate = 0.05
pull-coord2_k = 700
freezegrps = PPN
freezedim = Y Y Y
