GROMACS version: 2016.4
GROMACS modification: No
I am trying to pull a small molecule across a lipid bilayer. The bilayer is constructed using charmm-gui and the box is fixed the size of the lipid bilayer. During pull process, I end up with error “Distance between pull groups 1 and 2 (5.763902 nm) is larger than 0.49 times the box size (4.446700).”
So in case I have to increase the box size, can I do it before minimization and continue with the steps?
Or is there anything which I can add to the script to pull the molecule with the same dimensions as now?
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = POPC
pull_group2_name = POL
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.005 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
The Bilayer also consists of sterols.
Any suggestions would be really helpful