deformations in a cubic water box during equilibration in NAMD

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!

Rebeca García
Post-doctoral researcher
Universidad de Barcelona

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