Dear Amber users and experts,
I want to study the effect of different temperatures on structure and
flexibility of a protein containing 270 aa by MD simulation in explicit
solvent. Since I'm investigating the effect of temperature, I found it
difficult to chose the best way among several methods in heating and
equilibration which are presented in papers and tutorials.
So, I have a some questions about the heating procedure.
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)
2-Is it better to heat up the system directly (from beginning to final
temperature) or do it 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?
Any help would be greatly appreciated.
Thank you in advance,
M. Reza
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Received on Mon Sep 13 2010 - 10:30:04 PDT
