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

[Tsjerk Wassenaar]

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