On Wed, May 28, 2014 at 1:18 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> I've noticed that 3.6 kcal/mol is very small boost applied to all residues
> of my protein (400 a.a). Takng into account that this boost value have
> been saved in log after first 5000 timesteps of aMD but <DIHE> was
> reasonable big in comparison to cMD how I could make suggestions about
> reasonability of applied boost values ?
This is really a question that can only be answered through research.
What boost parameters are "reasonable" depends on what you want to
see. Keep in mind that recovering equilibrium properties by
reweighting via boost energies becomes less accurate as your boost
energy increases. You can reweight based on population, but I'm not
sure how that is affected by system size/boost energy magnitude. See
Markwick & McCammon, PCCP, 2011, 13, 20053-20065 and Sinko et al.,
JCPB, 2013, 117, 12759-12768 for more on aMD reweighting.
If you're not seeing the affect you want on a given timescale you can
adjust the boost parameters, but you may increase the overall noise in
your system. Alternatively, you could run a H-REMD simulation with
your lowest replica having no boost and the remaining replicas having
increasing amounts of boost, which implicitly takes care of the
reweighting for you (though you will probably have to play around with
the replica boost values to get reasonable exchange acceptance rates);
we have recently done this for an RNA tetranucleotide system (Roe et
al., JCPB, 2014, 118, 3543-3552).
If you haven't already, it is probably worthwhile to do a conventional
MD simulation so you have some sort of baseline to compare to.
-Dan
>
> James
>
>
> 2014-05-27 17:39 GMT+04:00 Daniel Roe <daniel.r.roe.gmail.com>:
>
>> Hi,
>>
>> On Sun, May 25, 2014 at 7:28 AM, James Starlight <jmsstarlight.gmail.com>
>> wrote:
>> >
>> > EAMD_BOOST = 3.6823
>> >
>> > does this value corresponded to the added dihedral term of all my system
>> or
>> > to one degree of freedom residue ?
>>
>> This is the total AMD boost applied to all dihedrals.
>>
>> -Dan
>>
>> >
>> > Also I'll be thankful if you provide me with some script suitable for
>> > calculation of averages of all output values like dihedral energy etc
>> >
>> >
>> > TFH,
>> >
>> > James
>> > _______________________________________________
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>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed May 28 2014 - 07:00:05 PDT
