[gmx-users] Concrete pull code explanation needed

Du, Yu duyu at sioc.ac.cn
Tue Jul 11 05:19:59 CEST 2017

Dear Justin and gmx users, 

I have gone through mdp-option and Justin A. Lemkul's COM pulling tutorial serveral times.

The following is Justin's pull code.

; Pull code
pull                    = yes
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = Chain_B
pull_group2_name        = Chain_A 
pull_coord1_type        = umbrella      ; harmonic biasing force
pull_coord1_geometry    = distance      ; simple distance increase
pull_coord1_groups= 1 2
pull_coord1_dim         = N N Y
pull_coord1_rate        = 0.01          ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
pull_coord1_start       = yes           ; define initial COM distance > 0

My understanding lists as follows, 

Justin defines two pull groups, with `pull-ngroups = 2`, each of them has a name in the index.ndx generated by `gmx make_ndx -f npt.gro`and their names are defined by `pull_group1_name = Chain_B` and `pull_group2_name = Chain_A`.

My question is about the definition of pulling coordination and the orientation of pulling force.

1) I learnt from [gmx-users] Change to umbrella sampling pull code,
"You need: pull-coord1-groups = 1 2 otherwise the reaction coordinate is undefined, or otherwise defaults to the entire system, I can't remember which. -Justin"

I know it's a plot :) in the input.pdb that proteins are placed exquisitely along the z-axis which is the same as the pulling coordinate but it makes pull code confused and here I need a concrete explanation.
1.The pull coordinate is the line that connects COM of group1 and group2 with `pull_coord1_groups= 1 2`. 
OR 2. The pull coordinate is the z axis with `pull_coord1_dim = N N Y`. 
Which is correct? 

2)Then turn to the orientation of pulling forces.
My understanding is that force1 acts on pull_group1, force2 acts on pull_group2 and the orientation of force 1 and 2 is opposite, both forces have a rate of 10nm per ns. 
Is my understanding and the below schematic draw right?


The last question is about the umbrella sampling.
I learnt from [gmx-users] Re: doubt about your Umbrella Sampling tutorial that it's ok to remove the pores of Chain B during the US. But in longer simulation time and in the periodical box, will the COM of Chain B and A be affacted by the boundary? and then affact the calculation of US potential?

Best Regards, 

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