Re: Basic question.

From: Taeho Kim (taehok_at_gurum.inje.ac.kr)
Date: Fri May 26 2006 - 22:03:20 CDT

Thank you peter for you reply..

If so, how long is it proper time for equilibration?
Now, I running 1ns and 1.5ns for equilibration, but it is very long I
think..

Peter Freddolino :
> Hi Taeho,
> to answer (2) first, equilibration is a short molecular dynamics
> simulation designed to relax the initial configuration; for example, it
> lets dipoles orient properly and water find more appropriate positions.
> The only technical difference is that it is sometimes carried out with
> restraints on part of the system (often the protein, for example). This
> step is necessary to avoid any artifacts that might show up from
> starting to take data from a system that is going to undergo quick
> relaxations such as this. I would highly recommend to you a textbook on
> molecular modelling techniques (such as Leach's /Molecular Modelling:
> Principles and Applications/) to have a look at the need for this step
> in more detail.
> Best,
> Peter
>
> Taeho Kim wrote:
>
>
>> Dear all.
>>
>> I have some basic question.
>>
>> 1. Why do we have to do equilibration step?
>> 2. What is different between equilibration and molecular dynamics?
>>
>> I have stuied about that by using Namd tutorial. I couldn't understand
>> clearly.
>>
>> Thank you.
>>
>> Best regards...
>>
>>
>>
>
>
>
>

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