AMBER Archive (2005)

Subject: AMBER: temprature and restraint in constant volumm MD

From: tonglei (xbcdnana_at_gmail.com)
Date: Mon Nov 21 2005 - 02:55:40 CST

 hello everyone
      How to control the velocity of raising temprature? When I tell
"sander" the velocity of raising temprature, for example : temprature
increase 50K every 5ps, but it didn't follow my command ,especially
the temprature can't raise to my expect temprature in the previous set
times (ps).
  When I didn't set the velocity of raising tempratue, the system can
dramatically from 0K raise to 300K at 14ps. Does this method bring
unreal changes of protein conformation?
  So I wonder how to control the velocity of raising temprature,
    what's the best one?
 In additon, a smaller restraint force is added on the protein in
amber tutorial. Is this restraint force neccessary? If neccessary ,
how about hold this smaller force only onto the Ca backbone atom?
  Thanks in advance 

--
 Na Zhang
 Chemistry Department
 Zhejiang University PRC
 xbcdnana_at_gmail.com
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