[gmx-users] Protein-surface interaction during flow

Christopher Neale chris.neale at alum.utoronto.ca
Tue Jan 31 17:25:45 CET 2017

Sorry if I was unclear. I was suggesting to continuously flow the solvent (probably can be done with standard gromacs options during a single run). The continuous flow will overcome the thermal noise issue. It won’t give you precisely the same as having a much longer system with some type of piston at the end that you push, but that sounds like a real nightmare system size so continuously flowing the water only (and not putting any artificial forces directly on the protein) might get you close to what you want.

— original message —

Christopher makes a good point.

Thermal motion will likely take over, but if you use a long enough initial push, you should also induce a local velocity field in the solvent around the protein which will allow some drifting. Alternatively you could give a kick to both the solvent and protein.

Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Christopher Neale <chris.neale at alum.utoronto.ca>
Sent: Tuesday, January 31, 2017 11:15 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] Protein-surface interaction during flow

flow the solvent and let the protein respond freely to that?

My guess is that the initial velocities will be lost fairly quickly to thermal noise if you try the suggestion of giving it a kick and then simply letting it go.

— original message —

I am trying to simulate a flow of protein over and along a surface
structure. To do this, I have a box which is very long in its x
direction, relatively small in its y direction and its z dimension is
limited by an artificially created surface. These proteins will move
in the positive x direction, starting at around x=0, and move towards
the surface structure. At this point the protein will either pass
along the structure, or adhere to it through LJ/Coulomb interactions.
There will also be interactions between the (many) proteins flowing.
Essentially, I’m trying to create a flow.

However, I’m unsure on how to do this. If I set the proteins as a
acc-grps, they will continue to accelerate even after they have
adhered to the surface, essentially pulling them off. Is there a way
to set acc-grps for a specific amount of time or distance? After which
their velocities will guide them towards the surface structure? Or can
I give these proteins a starting velocity after which they just flow?
Any ideas?

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