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. -- Gromacs Users mailing list
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