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

James Starlight jmsstarlight at gmail.com
Wed Apr 11 12:01:29 CEST 2012


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

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.


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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