[gmx-users] Re: Langevin Dynamics

[Dr. Vitaly Chaban]

If you have a correct temperature for the particle of interest,
everything is correct.



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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-- 
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