Hi,
>
> 1-Is it better to start heating from 0K or higher temperatures like 100K or
> 200K? (to prevent wild fluctuations and to be well equilibrated)
>
It is recommended to heat the system at 0-15K. Don't start with higher
temperatures for heating.
> 2-Is it better to heat up the system directly (from beginning to final
> temperature) or do it in several steps?
>
Yes you can do in several steps.
> 3-Is it better to heat up the system gradually (in a controlled manner
> nmropt=1) or as routine procedure?
>
4- how long should be sufficient for each step for a protein like this?
> Typically for initial heating do like 100-150 ps (NVT) and the another
> 800-900 ps (NPT) and then you can start equilibrating the system under your
> required conditions.
>
Manikanthan
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--
Manikanthan Bhavaraju
Graduate Teaching Assistant
Dept. of Chemistry
Mississippi State University
office no : 662-325-4633
MS -39762
USA.
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Received on Mon Sep 13 2010 - 11:30:04 PDT
