[gmx-users] Question about the pulling code

Tingguang.S tingguang.sun at gxust.edu.cn
Wed Sep 4 16:40:36 CEST 2019

Dear All,

I want to pulling a ligand out of the binding pocket using Gromacs 2019. The pulling code was:
pull                    = yes
pull_ncoords            = 1 

pull_coord1_type        = umbrella
pull_coord1_geometry    = direction
pull_ngroups            = 1
pull_group1_name        = Ligand
pull_coord1_dim         = Y N N
pull-coord1-vec         = 1 0 0

pull_coord1_rate        = 0.0005 
pull_coord1_k           = 830

I think the reaction coordinate had been defined by COM of the pulling group (i.e the ligand) and the pulling direction vector (i.e 1 0 0), but why still need to provide two groups for pull_coord1_groups ? If provided, then the reaction coordinate was also defined by the COM of the two groups, is this right?

How should I set up my pulling code with "pull_coord1_geometry    = direction". Any suggestion would be appreciated!

Best regards

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