I guess this is what you mean:
trajin cMDrun1.prod_TIP4PEw.nc
center :1-162 mass origin
image origin center familiar
trajout cMDrun1.prod_TIP4PEw.wrapped.nc netcdf
go
The protein residues are numbered 1-162. The trajectory doesn't change, it
seems that the barostast applies pressure over the 6 planes of a cube(?)
instead on the 12 planes of a truncated octahedron (?). There must be
something wrong with the parameters I am using because the .prmtop and .rst
files look normal to me. Below is the last line of my restart (.rst) file
from which I resumed the simulation. It was an NVT equilibration without
restraints.
115.6172820 135.3319607 138.3907610 90.0000000 90.0000000 90.0000000
I am also quoting again the relevant configuration parameters:
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
Any idea what's wrong?
Thomas
On 31 January 2013 14:54, David A Case <case.biomaps.rutgers.edu> wrote:
> On Thu, Jan 31, 2013, Thomas Evangelidis wrote:
> >
> > 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?
>
> Doens't sound like it. There are various ways to represent a truncated
> octahedron. If you want to view the results as an ocatahedron, use the
> "familiar" keyword in the image command in ptraj or cpptraj.
>
> ...dac
>
>
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>
--
======================================================================
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 - 12:30:04 PST
