Re: [AMBER] Different MMPBSA results in the use of sander and pmemd

From: Jason Swails <>
Date: Tue, 10 Sep 2013 07:06:06 -0400

On Mon, Sep 9, 2013 at 11:44 PM, ǧǧѰ <> wrote:

> hello, thank you for your reply. I have two different trajectories, one is
> done in sander, and the other in pmemd.I can get Jason's point. Maybe the
> two simulations could be exploring completely different regions of phase
> space.
> But in my system,the ligand binding to the protein has a Crystal Structure,
> I just want it to reach an equilibrium state. I think the Crystal Structure
> is stable,so i simulation 1ns in sander and pmemd, do you think it is
> enough?

No, it is probably not enough. That said, there may not be enough time for
the trajectories to diverge that much, either.

Have you visualized the trajectories to see how different they appear? You
should not try to discriminate based on MM/PBSA results, since they can be
misleading. How do the RMSDs compare? How do they compare to each other?
 Perhaps run decomposition per-residue in and compare the residue
contributions for each trajectory and see which residues differ the most.
 Then focus your investigations on those residues to see if they're doing
anything interesting.

These are all useful questions to ask yourself when investigating something
curious like this. (Also look at your standard deviation and standard
error of the mean -- if they overlap between the two trajectories then they
cannot be discriminated between statistically).

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 10 2013 - 04:30:02 PDT
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