Hello,
I ran a short simulation with pmemd.cuda using the following parameters but
the truncated octahedron was gradually reshaped to a parallelepiped box. Am
I doing something wrong?
ntxo=2, ! write binary NetCDF restart files
ioutfm=1, ! use binary NetCDF format for the coordinate and velocity
trajectory files (mdcrd, mdvel and inptraj).
iwrap=1, ! wrap coordinates into primary box
! TEMPERATURE CONTROL
tempi =100.0, ! initial temperature
temp0=300.0, ! reference temperature at which the system is to be
kept, if ntt > 0
ntt=3, ! Use Langevin thermostat.
gamma_ln=5, ! Damping coefficient for Langevin dynamics in ps - 1.
tautp=2.0, ! Time constant, in ps, for heat bath coupling for the
system, if ntt = 1
ig=209858, ! The seed for the pseudo-random number generator
! PRESSURE CONTROL
ntb=2, ! use constant pressure
ntp=1, ! use pressure coupling
thanks,
Thomas
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Thu Jan 31 2013 - 04:30:04 PST
