In the energy minimisation step, any "conformational rearrangement" taking place is not a function of time, it is just an algorithm for reaching a basin of minimum energy: <div><br></div><div>(<a href="http://www.gromacs.org/Documentation/Terminology/Energy_Minimisation">http://www.gromacs.org/Documentation/Terminology/Energy_Minimisation</a>), <div>
<br></div><div>hence there are not velocities in the atoms of the system, and macroscopic properties related to dynamics (like temperature) are not present.</div><div><div><br></div><div>Daniel Silva</div><div><br><br><div class="gmail_quote">
2011/10/17 bipin singh <span dir="ltr"><<a href="mailto:bipinelmat@gmail.com">bipinelmat@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
I have not understood what you mean by<br>
<div class="im">"Energy minimization is (theoretically) at 0 K, as there are no velocities<br>
and it is not a true dynamical process."<br>
</div>It is clear to me that at 0K there would be no velocities but then why<br>
during minimization we expect<br>
some conformational rearrangement of side chains etc.<br>
<div><div></div><div class="h5"><br>
<br>
On Mon, Oct 17, 2011 at 17:03, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
><br>
><br>
> bipin singh wrote:<br>
>><br>
>> As far as I know we do energy minimization at room temperature only.<br>
><br>
> Energy minimization is (theoretically) at 0 K, as there are no velocities<br>
> and it is not a true dynamical process.<br>
><br>
>> Only during equilibration<br>
>> (NVT and NPT) we use high temperature for maintaining proper density<br>
>> before starting the final production run.<br>
>><br>
><br>
> Maintaining density is but one possible goal for NPT; defining the desired<br>
> ensemble and therefore the sampling distribution is the main reason.<br>
><br>
> -Justin<br>
><br>
>> On Mon, Oct 17, 2011 at 15:15, Kavyashree M <<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>> wrote:<br>
>>><br>
>>> Dear users,<br>
>>><br>
>>> For simulating a protein at high temperature (more than 300K,<br>
>>> less than 400K) using OPLSAA forcefield, what are the parameters<br>
>>> other than Temperature that need to be taken care of?<br>
>>> Does the energy minimization step also needs to be done at high<br>
>>> temperature? (here my aim is not to simulate an unfolding event)<br>
>>> I have a reference -<br>
>>> Biophysical Journal Volume 94 June 2008 4444–4453<br>
>>><br>
>>> Any other references or suggestions will be helpful.<br>
>>><br>
>>> Thanking you<br>
>>> With Regards<br>
>>> M. Kavyashree<br>
>>><br>
>>><br>
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>>><br>
>><br>
>><br>
>><br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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><br>
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<br>
</div></div><div class="im">--<br>
-----------------------<br>
Regards,<br>
Bipin Singh<br>
</div><div><div></div><div class="h5">--<br>
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