From: AMIT PALIWAL (paliwal_at_jhu.edu)
Date: Tue Jan 06 2004 - 22:20:10 CST
I have had this problem with the new namd version 2.5. Whenever I simulate peptide in water- first minimize the system and then start the production run- in the production run, the total energy oscillates beween two levels very far apart. I can not understand why?? Minimization seems to be perfectly fine. There was a suggestion to use separate thermostats for peptide and water. if this is the problem then how do you go about doing this?
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