[AMBER] maintaining temperature scheme

From: <missing_grace.sina.com>
Date: Thu, 01 Jul 2010 12:05:21 +0800

&nbsp;Dear amber users,
When I follow the amber toturial and run MD ,the toturial1 recommend us to use the new Langevin temperature equilibration scheme(NTT=3) for maintaining the system temperature,other than NTT=1which is not very efficient at ensuring the temperature even across the system .
But when I turn to the tutrail3 (folding trp-cage peptide),I found when heating the system ,it use NTT=1 and&nbsp; tautp=1.0 to heat the system .
So I am confused ,why we should use NTT=1,not NTT=3 here. Are there many differences between these two schemes ?
Then&nbsp; I try to fold a small peptide(implicit water) , but I find there are big rmsd differences when use NTT=1 and NTT=3 respectively.
I thought that the method we use to heat the system should not influence the final result so much.I don't why it is ?
 could you explain it to me ?
Thank you very much !

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; yours
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; grace
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Received on Wed Jun 30 2010 - 21:30:03 PDT