From: ydhuang2727 (ydhuang2727_at_163.com)
Date: Mon Jun 29 2009 - 01:12:47 CDT
Yes, you are right, i should not have directly heated the protein up to 310K, which may cause problems. And i should heat gradually, to make the whole system approximately equilibrium. But from the namd tutorial, i did not find the more standard procedure, as you suggested, involving slowly heating system to the desired temperature. And i also feel surprise that you are so surprise, because i did not found anything wrong using "minimizing and then jumping to 310K", which is also definitely referred to in the namd tutorial.
I myself previously used a loop in the .conf file to heat the protein, which refers to increase the heat source temperature up to desired temperature 20K by 20K that does look proper way but takes time, you know. Since heating directly up to 310K got the same equilibrium state as step by step, i chose the former to save cost.
As your suggested standard procedure, i do have never seen anything about it.
Will you please offer us some information available.
Have you have any good advice on this problem.
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