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|                      NAMD 2.0 Release Notes                        |
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New Features in NAMD 2.0

- Reads CHARMM (or X-PLOR) formatted parameter files.

- Supports periodic and non-periodic MD simulations.

- Particle mesh Ewald full electrostatics for periodic simulations.

- Triple timestepping.

- Rigid bonds to hydrogen atoms.

- Fixed atoms implemented efficiently, no unnecessary force calculations.

- Berendsen and Langevin piston constant pressure methods.

- Steered Molecular Dynamics (SMD) features.



For problems or questions, send email to namd@ks.uiuc.edu.  If you
think you have found a bug, please include what machine you are
running on, and, if possible, a dump of the program output and/or a
copy of your input files.  Your feedback will help us improve NAMD2.


This File

This file contains brief instructions for running NAMD2.  For more
detailed information, see the users guide (ug.ps, in the doc directory).


Runing NAMD2

-- Workstation Networks --

Workstation networks require two files, the namd2 executable and the
conv-host program.  The conv-host program starts namd2 on the desired
hosts, and handles console I/O for the node programs.

To specify what machines namd2 will run on, the user creates a file
called "nodelist".  Below is an example nodelist file:

group main
 host brutus
 host romeo

The "group main" line defines the default machine list.  Hosts brutus
and romeo are the two machines on which to run the simulation.  Note
that conv-host may run on one of those machines, or conv-host may run
on a third machine.  The "rsh" command ("remsh" on HPUX) is used to
start namd2 on each of the nodes specified in the nodelist file.  If
NAMD fails without printing any output, check to make sure that "rsh"
works on your machine, by seeing if "rsh hostname ls" works for each
host in the nodelist.

A number of parameters may be passed to conv-host.  The most important
is the "+pX" option, where X specifies the number of processors.  If X
is less than the number of hosts in the nodelist, machines are
selected from top to bottom.  If X is greater than the number of
hosts, conv-host will start multiple processes on the machines,
starting from the top.  To run multiple processes on members of a SMP
workstation cluster, you may either just use the +p option to go
through the list the right number of times, or list each machine
several times, once for each processor.

Once the nodelist file is set up, and you have your configuration file
prepared (alanin.conf, in this example), run NAMD2 as follows:

conv-host +pX namd2 alanin.conf

Due to their processor design, Intel-based machines running the linux
version produce binary files (restart and DCD files) with a different
format.  The "flipbinpdb" and the "flipdcd" programs will convert
files back and forth from Intel format to the non-Intel format.

-- T3E --

The T3E version has been tested on the Pittsburgh Supercomputer Center
T3E.  To run on X processors, use the mpprun command:

mpprun -n X namd2 alanin.conf

-- Origin 2000 --

For small numbers of processors (1-8) use the non-MPI version of namd2.
To run on X processors call the binary directly with the +p option:

namd2 +pX alanin.conf

For better performance on larger numbers of processors we recommend
that you use the MPI version of NAMD2.  To run this version, you must
have MPI installed.  Furthermore, you must set two environment
variables to tell MPI how to allocate certain internal buffers.  Put
the following commands in your .cshrc/.profile file, or in your job
file if you are running under a queuing system:

setenv MPI_REQUEST_MAX 10240
setenv MPI_TYPE_MAX 10240

Then run NAMD2 with the following command:

mpirun -np X namd2 alanin.conf


NAMD2 Known Deficiencies

- PME does not parallelize well and has had limited testing.

- NAMD2 requires X-PLOR or CHARMM to produce the .psf structure input
files.  If you don't have one of these, you probably can't use NAMD2 yet.