[gmx-users] Pulling two groups in opposite direction

[Naba]

Dear all,

I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
acids from its homodimer in opposite directions along z axis. The
interfaces of each protein chain is parallel to the z axis. I do not need
any restraints in this case. I have gone through the GROMACS manual and
some of the previous archived messages and set the following mdp options.

; Pull code
pull                    = yes
pull_ngroups            = 2
pull_ncoords            = 2
pull_group1_name        = chain_A
pull_group2_name        = chain_B
;pull_group3_name = Protein
pull_coord1_type = umbrella
pull_coord2_type = umbrella
pull_coord1_init = 0.0
pull_coord2_init = 0.0
pull_coord1_start = yes           ; define initial COM distance > 0
pull_coord2_start = yes
pull_coord1_geometry    = direction
pull_coord2_geometry    = direction
pull_coord1_groups      = 2 1
pull_coord2_groups      = 1 2
pull_coord1_dim         = N N Y
pull_coord2_dim         = N N Y
pull_coord1_rate        = 0.01        ; 0.008 nm per ps = 8 nm per ns
pull_coord2_rate        = 0.01         ; 0.008 nm per ps = 8 nm per ns
pull_coord1_k           = 2000          ; kJ mol^-1 nm^-2
pull_coord2_k           = 2000
pull_coord1_vec        = 0.0 0.0 1.0
pull_coord2_vec        = 0.0 0.0 -1.0
nstcalcenergy = 1
nhchainlength = 1

But it fails to pull chain_A in positive z direction. However, chain_B is
seemed to pull in negative z direction. Someone please suggest the proper
way to pull two groups in opposite directions, or if there is anything that
I am missing.

waiting for your great help..
Nabajyoti Goswami
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India