Re: [AMBER] Protein "jumping" during SMD run

From: Carlos Simmerling <>
Date: Fri, 14 Sep 2018 16:32:53 -0400

Could this be imaging? Try turning it off during md if you haven't already.

On Fri, Sep 14, 2018, 11:13 AM Cory Ayres <> wrote:

> All,
> I am trying to run an SMD simulation and am noticing some odd behavior in
> the output. For context, I have two proteins and am trying to interrupt the
> interface. In order to have control of what direction I pull from, I've
> introduced a pseduoatom into the simulation. After locking the coordinates
> of the pseudoatom and protein 1, I decrease the distance from the CoM of
> protein 2 and the pseudoatom. Once I generate the simulation, I calculated
> the distance from the CoM of protein 2 and the pseudoatom, and as expected
> the distance does decrease. However, I notice large jumps along the
> reaction coordinate, sometimes jumps increasing and sometimes jumps
> decreasing the distance between the two. When visualizing the trajectory it
> genuinely looks massive changes in the actual coordinates of the protein.
> I had guessed that accessing the trajectory while it was still being
> written to was introducing these errors (ThreeAccess image) as every time I
> trajin'd the trajectory it would introduce a jump. As such, I started a new
> simulation that I didn't access expecting it to fix the issue, but I'm
> getting the same error. Does anyone have any thoughts as to what may be
> going on?
> Many Thanks,
> Cory Ayres
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Received on Fri Sep 14 2018 - 14:00:02 PDT
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