From: Hiroaki Maekawa (hmaekawa_at_uci.edu)
Date: Fri Oct 17 2008 - 16:37:16 CDT
Dear NAMD users,
I'm trying to equilibrate a peptide/solvent system under NVT after
a long NPT equilibration process (about 8 ns).
In the NPT process, the pressure and temperature is close to the target
values and hence
the NVT equilibration was started with the pressure control off and
using the restart.coor,
restart.vel, and restart.xsc files from the NPT run.
After for a while, it was found out that the pressure average is about
-20 bar, quite off from
the average value I got in the NPT (1 bar)
Is this just because it is not well equilibrated in the NPT yet?
Basically, I keep using the same parameters in the configuration file
and just comment out
the Langevinpiston and related parameters to it.
Or are there anything wrong in what I'm doing to do for the NVT
Thank you for your comments in advance
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