Hi
I tried to pull a ion through protein channel. But force is increasing exponentially with time which is quite unexpected. At some portion of channel force should have lowered. What could be the possible explanation?
I used 100 kjoule force and pulling distance is around 5nm .
In continuation of previous mail please find attached force plots for NAMD and gromacs. my pull parameters are
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = LIG
pull_group2_name = a_10042
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y ; pull along z
pull_coord1_groups = 1 2 ; groups 1 (Chain A) and 2 (Chain B) define the reaction coordinate
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 100 ; kJ mol^-1 nm^-2
it will be great if someone can guide me whats the difference in both pullings? why isnt energy lowering in gromacs?
