From: Dr. Eddie (eackad_at_gmail.com)
Date: Thu Jun 14 2012 - 21:33:27 CDT
I have a small (2700 atom) protein that is solvated and should be very
close to correctly folded. When I run the minimization on the solvated
system it seems to form a large air bubble. I am using pbc and waterWrap on
and at the end of my config file it has:
In the output from the run after the energy it prints:
REINITIALIZING VELOCITIES AT STEP 800 TO 310 KELVIN.
Yet the protein seems to be very cold and there is a large air bubble in
the system. This is not the "fake" bubble due to pbc (I see that one as
well). Even after 2 ns the bubble is still almost perfectly spherical.
Shouldn't it have reheated and given me something similar to when I don't
minimize? Has anyone had this problem and knows what I am doing incorrectly?
The protein's structure is almost identical after minimization yet there is
a large change in pressure and potential energy during minimization so I
assume almost all the minimization is coming from the water. Also I don't
see the bubble when I don't minimize.
I greatly appreciate any help. Thanks in advance!
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