GROMACS version: 2021.3
GROMACS modification: No
Hi everyone,
I am currently running steered MD simulation and it always gives the following error:
Fatal Error Distance between pull groups 1 and 2 (4.402440 nm) is larger than 0.49 times
the box size (4.402299).
The center of mass of MEMB is 4.60 nm and the center of mass of NPH is 6.88 nm. I tried changing the pull code with different options but it gave the same error. I am providing the mdp file below (the one I am currently using), thinking that you guys can help me. I would appreciate any suggestion. Thank you,
integrator = md
dt = 0.002
nsteps = 10000000
nstxout = 50000
nstvout = 50000
nstfout = 50000
nstcalcenergy = 100
nstenergy = 1000
nstlog = 1000
nstxout-compressed = 500
;
cutoff-scheme = Verlet
nstlist = 20
rlist = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
coulombtype = PME
rcoulomb = 1.2
;
tcoupl = Nose-Hoover
tc_grps = MEMB SOLV NPH
tau_t = 1.0 1.0 1.0
ref_t = 310.15 310.15 310.15
;
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
;
freezegrps = NPH
freezedim = Y Y N
;
nstcomm = 100
comm_mode = linear
comm_grps = System
;
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = MEMB
pull_group2_name = NPH
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = cylinder ; simple distance increase
pull_coord1_vec = 0.0 0.0 1.0
pull_coord1_dim = N N Y ; pull along z
pull-cylinder-r = 1.5 ;
pull-coord1-init = 2.0 ;
pull_coord1_groups = 1 2 ; groups 1 and 2 define the reaction coordinate
pull_coord1_start = no ; define initial COM distance > 0
pull_coord1_rate = -0.005 ; 0.01 nm per ps = 1 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2