[gmx-users] Pull group at constant speed

Lei xiaoainisa at gmail.com
Thu Feb 1 23:31:11 CET 2018

Hi, gmx users,
I have a question on pulling a group of molecules at a constant speed.
Let's say, I want move a protein in the vacuum at a constant speed of 0.01
nm/ps.  I am aware that I can specify the pull rate in the COM pulling. I
am using gromacs 5.1.2. Following is my pulling code:
;pull code
pull                              =  yes
pull-ngroups               =  1
pull-ncoords                =  1
pull-group1-name       =  protein
pull-coord1-type          =  umbrella
pull-coord1-geometry  = direction-periodic
pull-coord1-vec            =  1  0  0
pull-coord1-groups       =  0   1
pull-coord1-rate            =  0.01
pull-coord1-k                =  1000
However, this seems to be setting up the moving speed of the virtual spring
acting on the protein. I checked the mdpullx.xvg and used gmx traj to
calculate the velocity of the COM of the protein. It is apparently not
moving at the speed that I wanted. So I am wondering if there is a way to
pull the protein at a constant speed?
Thank you  all for your attention.

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