Hi Jef, Hi Sourav,
Maybe I can comment further here ...
We did quite a bunch of aMD (only dihedral boost) runs on
protein/nucleic acid complexes (not published yet) and I can confirm
that it works well at least qualitatively. Using parameters calculated
based on the suggestions on the amber manual (3.5 kcal/mol/residue to
estimate alpha and Ed) did not affect DNA much. However, adding 2 alphas
to the boost did destroy the DNA at the ends on some of our systems.
However, the problem came when we tried to reweight. We realized that
the boost was far too high for reweighting even using the second order
cumulant expansion.
We came across this paper that I mentioned in my previous email ...
http://www.ncbi.nlm.nih.gov/pubmed/23781107 and we switched to apply the
lambda-based scheme for estimating the parameters. The paper suggests
lambda=0.3 for the protein/membrane system they investigated. However,
we found 0.3 to be too large or our systems as the reweigthing was still
compromised. We now switched to test different lamdas and a value of
0.15 appears to give very nice trajectories that sample significantly
more the dynamics of the systems compared with standard MD and can also
be reweighted. However, we also noticed that in order to get smooth
profiles upon reweighting we need to run quite long simulations (150 ns
is by far not enough as the reweighted profiles are still noisy).
This is to share our experience with the particular systems we work
with. Whether this is applicable to other system, I don't know.
So,please test for any different system. But I would definitely
recommend the lambda-based scheme to estimate the parameters (its only 1
variable to be changed, and therefore easier to run tests with)...
I hope this helps
Vlad
On 04/27/2014 09:16 PM, Jeff Wereszczynski wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Sun Apr 27 2014 - 15:00:02 PDT
