From: Fabio Zegarra (fabiozegarra7_at_gmail.com)
Date: Tue May 06 2008 - 15:44:53 CDT
Dear NAMD users:
I am equilibrating a small protein (NPT simulation , 1 nanosecond). The
protein is in a water box (with around 8000 water molecules) with periodic
boundary conditions, and I am using the following parameters to control the
temperature and pressure.
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp 300
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Constant Pressure Control
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
To check the simulation I calculated the average temperature and pressure in
the *.log file, the average temperature is around 299 K, but the average
pressure is around -20 bar . To make sure I also used other parameter
values, but the results were the same (negative average pressure). I want to
know if this is right or I have to change something in the control
parameters.
Sincerely,
Fabio
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