Re: [AMBER] weird output of SMD simulation combined with Constant pH

From: Jason Swails <>
Date: Mon, 7 Dec 2015 09:29:41 -0500

On Mon, Dec 7, 2015 at 9:25 AM, zhonghe xu <> wrote:

> Hi Amber Users:
> I used Amber14 to run SMD (jar) simulations combined with explicit solvent
> constant pH.
> I also analysed the distance between pulling group and reference group
> using distance
> command in cpptraj module. Then I found the results (distance vs time)
> obtained from analysis of
> trajectory are severely deviated from standard output of jar, which can be
> seen in below figure.
> By the way, I also excluded periodic boundary condition (image) effect
> during analysis the distance,
> and the aforementioned problem was never found in previous SMD (jar)
> simulations without constant pH
> for same system.

​Oh, yea, this might not work. I've never tried it. The problem is
probably that the relaxation dynamics is confusing the steering potential.
This is probably not going to be an easy thing to fix (the way I will
probably fix it for now is to tag this combination as unsupported and make
it quit).

I suggest using umbrella sampling instead, which should work fine.

Thanks for the report,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Dec 07 2015 - 06:30:06 PST
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