[gmx-users] setting up a pull vec

Christopher Neale chris.neale at alum.utoronto.ca
Sat Nov 26 03:34:14 CET 2016

You haven't told us what you want to do, but perhaps you want to pull them apart along the vector that connects the centers of mass of these two species. One possible way to do that is to use gmx traj -com to get the two centers of mass, then figure out the vector yourself. That's going to get messy if the whole complex tumbles in solution, so you could also add a few absolute position restraints to pin down one of the molecules.

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of abhisek Mondal <abhisek.mndl at gmail.com>
Sent: 25 November 2016 02:37:18
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] setting up a pull vec


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

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


Abhisek Mondal

*Research Fellow*

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

*Kolkata 700032*

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