[gmx-users] Re: Langevin Dynamics

[Justin Lemkul]

On 12/14/12 12:40 PM, Dr. Vitaly Chaban wrote:
> If you have a correct temperature for the particle of interest,
> everything is correct.
>

One important caveat, of course, is a given thermostat's ability to produce 
velocities that belong to a real NVT ensemble.  This is not the case, for 
instance, with the Berendsen algorithm.  It maintains the temperature, but the 
distribution is not canonical.  If the goal is simply to heat up a given species 
and then proceed with further simulations, the method chosen during heating is 
probably rather insignificant.

-Justin

>
>
> On Fri, Dec 14, 2012 at 6:38 PM, tarak karmakar <tarak20489 at gmail.com> wrote:
>> Thanks Dr. Vitaly
>>
>> Yeap !
>>
>>  From that point of view I'm seeing the correct temperature drift and
>> it reaches nicely to 300 K after say, 300ps.
>> But is it a good integrator ( SD ) to perform this job ? Or, should I
>> opt for other, like Lep-frog or MD-VV with let say , Berendsen
>> thermostat?
>> Please explain a bit.
>>
>> Thanks
>> Tarak
>>
>> On Fri, Dec 14, 2012 at 10:44 PM, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:
>>>>
>>>> I am going to do US simulation in a protein. For this purpose I have
>>>> heated the protein from 0 to 300 K by using 'SD' integrator. But I am
>>>> bit confused with this integrator.
>>>> How good is to use Langevin Dynamics to heat a protein ?
>>>>
>>>
>>>
>>> Look at the temperature of protein and decide.
>>>
>>>
>>> Dr. Vitaly V. Chaban
>>> MEMPHYS - Center for Biomembrane Physics
>>> Department of Physics, Chemistry and Pharmacy
>>> University of Southern Denmark
>>> Campusvej 55, 5230 Odense M, Denmark
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>
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
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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