Hi Sourav,
I haven't looked at the suggestions in the Amber user guide, but I have a
pretty good guess as to what they are. It sounds like you are doing a
"dual-boost" setup. So here's what I would say.
1. Yes. The number of atoms is typically used for the term that boost the
complete potential, which is dominated by non bonded terms. Since waters
are included in that, you need to include the water atoms.
2. As far as I know, no one has published aMD simulations with nucleic
acids. I've played with it a bit, and it works fine. You should include
the DNA in the residue count since they are being accelerated by the
dihedral term (since they have dihedrals in them). Just keep in mind that
the suggested aMD parameters were derived mainly for proteins with the
amber force field, so you may need to fiddle with the acceleration
parameters you use. But the suggestions in the amber user guide should get
you in the right ballpark.
Typically what you want to do is try a number of short simulations with
different parameters, using the parameters in the amber user guide as a
suggestion, then seeing how it affects your system. If you need more
acceleration, try adding a value of alpha (or alphaD) to your thresholds.
If you have too much acceleration and you are getting unphysical effects,
decrease your thresholds by alpha. Other people have different
parameterization methods, but in the past this has worked well for me.
Cheers,
Jeff Wereszczynski
Assistant Professor of Physics
Illinois Institute of Technology
http://www.iit.edu/~jwereszc
> Message: 2
> Date: Sun, 27 Apr 2014 16:31:08 +0530
> From: Sourav Purohit <sour000.gmail.com>
> Subject: [AMBER] Accelerated MD
> To: AMBER Mailing List <amber.ambermd.org>, Jason Swails
> <jason.swails.gmail.com>, ross.rosswalker.co.uk
> Message-ID:
> <CAFMrzpzPjf1ZN2-V71v=fkeZrDeGNytZsAQSpL7ZxM1xysvs=
> w.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi all,
>
> I had some doubts on the method of calculating parameters for accelerated
> MD as described in the AMBER12 manual (page no.160).
>
> 1.Does the total number of atoms (taken as 16950 in the example) include
> atoms belonging to water molecules also??
>
> 2.for the calculation of alphaD, only the number of protein residues goes
> as an input. What if a system has other components like DNA?? Should I
> include the DNA residues also??
>
> Kindly help.
>
> Thanks.
>
>
>
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Received on Sun Apr 27 2014 - 12:30:02 PDT
