[gmx-users] Protein-surface interaction during flow

Smith, Micholas D. smithmd at ornl.gov
Mon Jan 30 15:29:46 CET 2017

Hi Mark,

There are two ways I see you could do this:

1) Perform multiple simulations at different accelerations (i.e. different applied forces)
2) Pick the acceleration you want, start a simulation, calculate the velocity of your protein every few steps, and once you have it, then stop, and use the velocities and positions at the end of the initial "push" segment as new initial conditions for a new run without the accel. group.

The first choice is something akin to dragging the protein across the surface (in which case you could likely use the pull code with you setting a maximum pull-force) and you can measure/quantify the adherence strength directly. The second choice using a prolonged impulse. 

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 Kamps, M. <m.kamps at student.rug.nl>
Sent: Monday, January 30, 2017 9:17 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Protein-surface interaction during flow

Dear GMX users,

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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