[gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

Tsjerk,


As Justin already has noticed there were lot of examples of implementation
of the high temperature aproach to increase conformation sampling. This
could be usefull because of short time-scale of typical MD trajectory and
hight energy barriers of the adjacent energy-minimums wich could correspond
to the functional-relevant conformations.  So the main reason of such
stimulations in to dicrease such barriers to promote transitions to the
functional-relevant states conformations Finally I can sample the output of
such simulation and compare this resulted conformations with the
experimental data. If I obtain good similarity this may indicate about
efficiency of such aproach

On other hand such simulation could result in some non-native conformations
due to the non-native condtions. So the artificial restrains like as the
distance restrains within native conformation ( obttained by NMR for
instance) could be usefull-aproach to keep the system in the native-like
conformations while enhansing sampling of the native-like structures via
rising of temperatures. So combinations of  such tricks could give
physical-relevant results partly couldn't it ? However I suppose that the
main disadvantage of such aproach is the non-physical intermediate states
produced by non-native transitions pathways wich could arrise from such
simulation.



James

11 апреля 2012 г. 18:09 пользователь Tsjerk Wassenaar
<tsjerkw at gmail.com>написал:

> Hey James,
>
> Have you thought about the physical relevance of your results?
>
> Cheers,
>
> Tsjerk
>
> On Wed, Apr 11, 2012 at 12:01 PM, James Starlight
> <jmsstarlight at gmail.com> wrote:
> > Tsjerk,
> >
> > Thank you for suggestions!
> >
> >
> > Indeed the hight temperature ( I'm using 700K) which I use for enhansing
> > sampling rate  resulted in destabilisation of the secondary structure.
> >
> > To prevent this I've used two slightly different aproaches based on the
> > restraint. But in both cases I've used slightly soft restrains with
> > fs=10-200.
> >
> > The first aproach is the ussage of the posres applied on each backbone
> atom
> > with fc=10-50. I've tested case with fc=50 and found that such restrains
> > were very hight. I've not noticed any conformation sampling of my
> protein (
> > rmsd of backbone < 0.3 nm) during 10ns of such simulation. So I've
> decided
> > to test a case with fc=10 ( under calculation)
> >
> > The second approach is the application of the harmonic distance
> restrainse
> > wich I've applied on each backbone atom pair in the CUTOFF radius of 1.0
> nm.
> > The Rc value was chosen because of my protein is the 7 buddle of alpha
> > helices so this aproach could be usefull but exactly value for R have
> been
> > chosen empirically. I've selected deviation value wich are equal to 1\2
> of
> > cutoff radius = 1.5 nm. I have not realise whaat I could obtain yet from
> > this because I'm not quite sure about coccect values of such disres.
> >
> >
> > James
> >
> > 11 апреля 2012 г. 13:35 пользователь Tsjerk Wassenaar <tsjerkw at gmail.com
> >
> > написал:
> >>
> >> Hey :)
> >>
> >> I'd say a protein should be loosing structure at 700K. Can't even say
> >> the force field is wrong there, even though it hasn't been
> >> parameterized for such temperatures for certain. You'd have to check
> >> with experiments.
> >> Trying to do high-temperature simulations is fine. But trying to do
> >> high temperature simulations to get results that match a room/body
> >> temperature ensemble is completely bogus. If you aim to use this
> >> approach for enhanced sampling, you're in for some serious
> >> reparameterization. Part of the deal may indeed be adding
> >> long(er)-range distance restraints. However, the force constants to
> >> use will increase with temperature, and with very high temperatures
> >> the force constants may end up so high that they give rise to fast
> >> oscillations, which will require using a smaller time step.
> >>
> >> Just my 2 cents...
> >>
> >> Tsjerk
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >>
> >> post-doctoral researcher
> >> Molecular Dynamics Group
> >> * Groningen Institute for Biomolecular Research and Biotechnology
> >> * Zernike Institute for Advanced Materials
> >> University of Groningen
> >> The Netherlands
> >> --
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> >
> >
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing list    gmx-users at gromacs.org
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