08 September 2020 8 5K Report

Dear all,

I am looking for a way to restrain the center of mass (COM) of two different molecules bathed in water, using GROMACS 2018. The only thing close I found on gromacs that does this is the pull module embedded in the mdp files. I want to clarify that I want to restrain each molecules (COM) to a different and specific coordinate in my simulated box. Indeed the pull module has an option - pull-coord1-geometry = direction, where I can set the origin (pull-coord1-origin= 0 0 0, for example) and a vector directing the movement of the COM (pull-coord1-vec= 1 1 1) with time (pull-coord1-rate = 0.01nm/ps). However I don’t want my COM to move in time, I want it stationary in a specific coordinate throughout my entire simulation time. I see that I can set a parameter - pull-coord1-start = no - so that it doesn’t start moving towards my vector and stays in what I labeled “origin”.

With all that said, when running my simulations, it looks like my specification in the mdp file lead to no restraints, and it looks like my molecules defuse freely without an energetic bias towards my specified origin coordinate. Here are my mdp settings:

pull = yes pull-ngroups = 2 pull-group1-name = NAH pull-group2-name = RAT

pull-ncoords = 2

pull-coord1-type = umbrella pull-coord1-geometry = direction pull-coord1-groups = 0 1 pull-coord1-dim = Y Y Y pull-coord1-origin = 3.75 2.5 2.5 pull-coord1-vec = 1.0 1.0 1.0 pull-coord1-k = 10000.0 pull-coord1-rate = 0.0 pull-coord1-init = 0 pull-coord1-start = no

pull-coord2-type = umbrella pull-coord2-geometry = direction pull-coord2-groups = 0 2 pull-coord2-dim = Y Y Y pull-coord2-origin = 3.75 2.5 2.5 pull-coord2-vec = 1.0 1.0 1.0 pull-coord2-k = 10000.0 pull-coord2-rate = 0.0 pull-coord2-init = 0 pull-coord2-start = no

where pull-coord2-init = 0 is supposedly irrelevant to the “direction” type of pulling.

If anybody has any experience with this pulling direction technique and might point me to where my settings are wrong, Id be extremely thankful.

Best to all, Ilan Shumilin

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