Date: Thu Nov 02 2006 - 08:52:39 CST
I have problems in the equilibration of a protein using NAMD. I have
tried lots of trial&error and this is what I have seen.
-When I apply constant pressure and restraints in all the protein, the
water box is not deformed, but in the next step I cannot take off the
restraints because errors related to RATTLE appear.
-When I apply constant volume (flexibleCell no), the equilibration
ends without error but the water box is deformed (the vertices are not
squared, the walls are not rectiline,...)
-I tried also changing the way of heating the system (langevin off and
reassignFreq, reassignTemp, reassignIncr,...; langevin on,...), but no
I have seen that some people have had this problem, too, but I havent
found the solution. Can anybody help me?
Thanks a lot in advance!
Universidad de Barcelona
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