[gmx-users] Pulling two groups in opposite direction

[Justin Lemkul]

On 5/16/18 3:32 AM, Naba wrote:
> 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

Note that pull_coord*_dim is not relevant when using "direction" geometry.

> 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.

What is the point of pulling in two directions? Separation of two 
species requires only one reaction coordinate. For every action, there 
is an equal, but opposite reaction...

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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