Re: NAMD restarts binary files

From: LEWYN LI (
Date: Wed Oct 12 2005 - 11:27:01 CDT


         The restart .conf file will be very similar to your original
.conf file. You need to change the following things:

1. Comment out the line which specifies the temperature of your system,
because the system temperature will now be determined by your restart
.vel file.

2. After "coordinates", type in the name of your restart .coor file if
the file is in ASCII. If your .coor file is binary, use "bincoordinates".
Note that if you used "bincoordinates", you still need to type in
something like:

coordinates something.pdb
bincoordinates real_binary_restart.coor

But the coordinates in "something.pdb" will be ignored.

3. Also type in:

binvelocities the_velocity_restart_file.vel

Use "velocities" instead of "binvelocities" if your .vel file is in ASCII.

4. Change the names of the output files so that the output from your
crashed run would not be overwritten.

5. (Optional) Change the "firsttimestep" to the time step corresponding
to your restart .coor and .vel files.

         You can then re-start your NAMD run with the new .conf file.

         Hope this helps.


On Wed, 12 Oct 2005, snoze pa wrote:

> Hi,
> I was running namd for 2 ns and my simulation crashed at 1.5ns. How can I
> restart my simulation from 1.5ns? is there any change in configuration file.
> I am also writing all restart coordinates and velocites after every 1000.
> Anybody canprovide me a small portion of conf file where I can add my
> restart coordinates and velocites.
> thanks in advance
> snoze

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:14 CST