[gmx-users] setting up a pull vec

[abhisek Mondal]

Hi,

I'm trying to run a umbrella sampling using following pull code:
; Pull code
pull                    = yes
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = JZ4
pull_group2_name        = Protein_chain_A
pull_coord1_type        = umbrella      ; harmonic biasing force
pull_coord1_geometry    = direction-periodic
pull_coord1_groups      = 1 2
pull_coord1_dim         = Y Y Y ; pulling in all dimension
pull_coord1_rate        = 0.01          ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k           = 500           ; kJ mol^-1 nm^-2
pull_coord1_start       = yes           ; define initial COM distance > 0

This approach needs me to specify a pulling vec which is essentially not
0,0,0.

Could you please suggest me a way to decide how to provide the pull vec ?

Thanks.

-- 
Abhisek Mondal

*Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*