Re: [AMBER] ScaledMD for proline dipeptide

From: Niels Geudens <>
Date: Mon, 04 Aug 2014 14:20:59 +0200


I indeed found an error in the parameters of my dipeptide. After
mending the problem, the simulation runs without any problems! Thank
you for your help.

One last question though: I would like to calculate the relative
presence of the isomers, but can I just use the trajectory as such, or
do I need to run the reweighting algorithm using the scaledMD.log-file?
What exactly is the scaledMD.log file?

Kind regards


Quoting Jason Swails <>:

> On Fri, Jul 18, 2014 at 12:55 AM, Niels Geudens <>
> wrote:
>> What a nice expression: NaNdyland.. :)
>> I used pmemd.sander or cuda (single GPU) for the simulation, all of
>> them blew up. I will reparameterize the molecule and see what happens.
>> If it still goes wrong, I will let you know!
> ‚ÄčIt's not necessarily the parametrization. Common things to look for are
> atoms with zero vdW parameters (mainly hydroxyl hydrogens in the Amber
> force field) that can collapse into another atom. Atoms with zero mass
> (that are not extra points fixed to a particular frame of reference)
> (although this would result in an immediate failure). There are not too
> may things that can give rise to NaN's, and simply rerunning antechamber is
> unlikely to be productive (unless you didn't check your parameters at all
> and a bunch of them are 0's because parmchk couldn't determine suitable
> substitutes).
> It's also possible that your lambda value is too small, and the potential
> energy surface is flattened too much in some region (have you tried
> different values of lambda?).
> Another thought is to specify a value of lambda that is formally equivalent
> to standard MD. According to the paper, setting lambda=1 should result in
> a PES that is effectively unscaled (so I think you should get standard NVT
> behavior), but still should traverse the scaledMD code. Of course it would
> seem that scaledMD documentation is rather lacking in the Amber 14 manual
> -- I see only mention that it is a new feature in pmemd, to say nothing of
> how to actually use it. But see if you get crashes with standard MD as
> frequently as you got crashes with scaled MD. Then try turning on scaledMD
> and set the lambda value to 1 and make sure it still behaves like standard
> NVT dynamics.
> Then start changing that input to match the one that fails for you.
> Hopefully that could help narrow down the input that's causing the
> problems (if indeed it is an issue with an input parameter or a bug in the
> code). That'll either help you determine what parameters you should change
> or give the scaled MD code maintainers a hint about where to look for a bug.
> Hope this helps,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER mailing list

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Received on Mon Aug 04 2014 - 05:30:02 PDT
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