[gmx-users] High temperature Simulation

[Mark Abraham]

On 17/10/2011 10:58 PM, bipin singh wrote:
> I have not understood what you mean by
> "Energy minimization is (theoretically) at 0 K, as there are no velocities
> and it is not a true dynamical process."
> It is clear to me that at 0K there would be no velocities but then why
> during minimization we expect
> some conformational rearrangement of side chains etc.

There's still an energy, and we can compute its gradient with respect to 
atomic coordinates, i.e. forces. EM algorithms move the atoms according 
to those forces to see a stationary point on the potential energy 
surface. MD algorithms use the forces to update velocities and 
positions, integrating Newton's second law with a finite time step.

Mark

>
>
> On Mon, Oct 17, 2011 at 17:03, Justin A. Lemkul<jalemkul at vt.edu>  wrote:
>>
>> bipin singh wrote:
>>> As far as I know we do energy minimization at room temperature only.
>> Energy minimization is (theoretically) at 0 K, as there are no velocities
>> and it is not a true dynamical process.
>>
>>> Only during equilibration
>>> (NVT and NPT) we use high temperature for maintaining proper density
>>> before starting the final production run.
>>>
>> Maintaining density is but one possible goal for NPT; defining the desired
>> ensemble and therefore the sampling distribution is the main reason.
>>
>> -Justin
>>
>>> On Mon, Oct 17, 2011 at 15:15, Kavyashree M<hmkvsri at gmail.com>  wrote:
>>>> Dear users,
>>>>
>>>> For simulating a protein at high temperature (more than 300K,
>>>> less than 400K) using OPLSAA forcefield, what are the parameters
>>>> other than Temperature that need to be taken care of?
>>>> Does the energy minimization step also needs to be done at high
>>>> temperature? (here my aim is not to simulate an unfolding event)
>>>> I have a reference -
>>>> Biophysical Journal Volume 94 June 2008 4444–4453
>>>>
>>>> Any other references or suggestions will be helpful.
>>>>
>>>> Thanking you
>>>> With Regards
>>>> M. Kavyashree
>>>>
>>>>
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>>>
>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
>