Re: [AMBER] The output file about SMD

From: Jason Swails <>
Date: Sat, 9 May 2015 11:37:57 -0400

On Sat, May 9, 2015 at 9:24 AM, wjli <> wrote:

> Dear Amber members,
> I know SMD is quite complex and I am effectively a novice.
> RST fle:
> &rst iat=507,503, r2=8.8, rk2=1.0725, r2a=5.8 /
> I just dont understand what do the four columns of the output file mean:
> 15.00500 14.75768 2470.68119 3.07782
> 15.01000 15.13490 -1246.46571 6.13835
> ……
> I guess x0 means the initial distance of the short time window,x is the
> final distance,the force is the mean force of the short time window,but the
> work is of the entire process?What about the plus or minus of the force(the
> direction is from residue 507 to 503)?

​The columns are, in order, the target reaction coordinate (RC) value for
that step​, the *actual* value in the simulation along the RC for that
step, the force imposed by the umbrella potential along the RC, and finally
the work done by the restraint at that point.

Notice that the sign indicates which "direction" along the RC the potential
is pulling your system. In the first line, the actual RC is less than the
target value, so the force is pulling it in the positive direction. On the
second line, the actual RC is greater than the target value, so the force
is pulling it "backwards" in the negative direction.

If I want just move residue 507(it is an ion ),what should I do ?Fix the
> whole protein ?

​What I've done in the past is just define a reaction coordinate as a
distance between the small molecule (or ion) and some residue it interacts
with closely in the bound state, then increase that distance to "pull" the
ion away from its active site.

I simply want to know whether the ion can go through the tunnel and reach
> the active
> site.I will very appreciate if anyone can offer more details about SMD
> using AMBER or related papers.

​"Pushing" an ion into an active site is a lot more challenging than
pulling one out, so it may be worth considering the reverse process instead.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sat May 09 2015 - 09:00:02 PDT
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