Hi Thomas,
We only consider the DIHED energy.
Best,
Vlad
On 04/28/2014 11:42 PM, Thomas Evangelidis wrote:
> Hi guys,
>
> Jason made a good point in another thread about ff14ipq. The _true_ torsion
> potentials are actually the sum of the dihedral energy plus the 1-4 vdW and
> 1-4 electrostatic energies as well. I wonder how you calculate the "average
> dihedral energy" from AMBER output to decide the aMD dihedral boost value.
> Do you count only the "DIHED" values or the "1-4 NB" and "1-4 EEL" too?
>
> thanks,
> Thomas
>
>
> On 28 April 2014 08:15, Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>wrote:
>
>> Hi Thomas,
>>
>> Well, the reweighted profiles for different structural properties were
>> very noisy and therefore useless.
>> See Daniel's answer as well.
>>
>> Vlad
>>
>> Sent from my android device.
>>
>> -----Original Message-----
>> From: Thomas Evangelidis <tevang3.gmail.com>
>> To: AMBER Mailing List <amber.ambermd.org>
>> Sent: Mon, 28 Apr 2014 1:30 AM
>> Subject: Re: [AMBER] Accelerated MD
>>
>> Hi Vlad,
>>
>> How did you decide that the trajectories could not be reweighted?
>> Στις 28 Απρ 2014 12:53 ΠΜ, ο χρήστης "Vlad Cojocaru" <
>> vlad.cojocaru.mpi-muenster.mpg.de> έγραψε:
>>
>>> 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.
>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> 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
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 28 2014 - 16:30:02 PDT
